Full text data of YBX1
YBX1
(NSEP1, YB1)
[Confidence: medium (present in either hRBCD or BSc_CH or PM22954596)]
Nuclease-sensitive element-binding protein 1 (CCAAT-binding transcription factor I subunit A; CBF-A; DNA-binding protein B; DBPB; Enhancer factor I subunit A; EFI-A; Y-box transcription factor; Y-box-binding protein 1; YB-1)
Note: presumably soluble (membrane word is not in UniProt keywords or features)
Nuclease-sensitive element-binding protein 1 (CCAAT-binding transcription factor I subunit A; CBF-A; DNA-binding protein B; DBPB; Enhancer factor I subunit A; EFI-A; Y-box transcription factor; Y-box-binding protein 1; YB-1)
Note: presumably soluble (membrane word is not in UniProt keywords or features)
UniProt
P67809
ID YBOX1_HUMAN Reviewed; 324 AA.
AC P67809; P16990; P16991; Q14972; Q15325; Q5FVF0;
DT 11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
read moreDT 23-JAN-2007, sequence version 3.
DT 22-JAN-2014, entry version 116.
DE RecName: Full=Nuclease-sensitive element-binding protein 1;
DE AltName: Full=CCAAT-binding transcription factor I subunit A;
DE Short=CBF-A;
DE AltName: Full=DNA-binding protein B;
DE Short=DBPB;
DE AltName: Full=Enhancer factor I subunit A;
DE Short=EFI-A;
DE AltName: Full=Y-box transcription factor;
DE AltName: Full=Y-box-binding protein 1;
DE Short=YB-1;
GN Name=YBX1; Synonyms=NSEP1, YB1;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=2977358; DOI=10.1016/0378-1119(88)90514-8;
RA Sakura H., Maekawa T., Imamoto F., Yasuda K., Ishii S.;
RT "Two human genes isolated by a novel method encode DNA-binding
RT proteins containing a common region of homology.";
RL Gene 73:499-507(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=3174636; DOI=10.1073/pnas.85.19.7322;
RA Didier D.K., Schiffenbauer J., Woulfe S.L., Zacheis M., Schwartz B.D.;
RT "Characterization of the cDNA encoding a protein binding to the major
RT histocompatibility complex class II Y box.";
RL Proc. Natl. Acad. Sci. U.S.A. 85:7322-7326(1988).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=1891370; DOI=10.1093/nar/19.17.4771;
RA Kolluri R., Kinniburgh A.J.;
RT "Full length cDNA sequence encoding a nuclease-sensitive element DNA
RT binding protein.";
RL Nucleic Acids Res. 19:4771-4771(1991).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Bone marrow;
RX PubMed=8188694;
RA Horwitz E.M., Maloney K.A., Ley T.J.;
RT "A human protein containing a 'cold shock' domain binds specifically
RT to H-DNA upstream from the human gamma-globin genes.";
RL J. Biol. Chem. 269:14130-14139(1994).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Adrenal cortex, Eye, Kidney, Muscle, Placenta, Skin, Testis,
RC and Uterus;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [6]
RP PROTEIN SEQUENCE OF 2-53; 70-93; 102-137; 157-185; 205-231; 257-279
RP AND 305-324, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2,
RP PHOSPHORYLATION AT SER-165, AND MASS SPECTROMETRY.
RC TISSUE=Ovarian carcinoma;
RA Bienvenut W.V.;
RL Submitted (JAN-2010) to UniProtKB.
RN [7]
RP FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
RX PubMed=10817758;
RA Chen C.-Y., Gherzi R., Andersen J.S., Gaietta G., Juerchott K.,
RA Royer H.-D., Mann M., Karin M.;
RT "Nucleolin and YB-1 are required for JNK-mediated interleukin-2 mRNA
RT stabilization during T-cell activation.";
RL Genes Dev. 14:1236-1248(2000).
RN [8]
RP FUNCTION.
RX PubMed=11698476;
RA Capowski E.E., Esnault S., Bhattacharya S., Malter J.S.;
RT "Y box-binding factor promotes eosinophil survival by stabilizing
RT granulocyte-macrophage colony-stimulating factor mRNA.";
RL J. Immunol. 167:5970-5976(2001).
RN [9]
RP FUNCTION, INTERACTION WITH SFRS9, AND SUBCELLULAR LOCATION.
RX PubMed=12604611; DOI=10.1074/jbc.M212518200;
RA Raffetseder U., Frye B., Rauen T., Juerchott K., Royer H.-D.,
RA Jansen P.L., Mertens P.R.;
RT "Splicing factor SRp30c interaction with Y-box protein-1 confers
RT nuclear YB-1 shuttling and alternative splice site selection.";
RL J. Biol. Chem. 278:18241-18248(2003).
RN [10]
RP INTERACTION WITH SFRS12.
RX PubMed=14559993; DOI=10.1128/MCB.23.21.7437-7447.2003;
RA Li J., Hawkins I.C., Harvey C.D., Jennings J.L., Link A.J.,
RA Patton J.G.;
RT "Regulation of alternative splicing by SRrp86 and its interacting
RT proteins.";
RL Mol. Cell. Biol. 23:7437-7447(2003).
RN [11]
RP INTERACTION WITH ANKRD2.
RX PubMed=15136035; DOI=10.1016/j.jmb.2004.03.071;
RA Kojic S., Medeot E., Guccione E., Krmac H., Zara I., Martinelli V.,
RA Valle G., Faulkner G.;
RT "The Ankrd2 protein, a link between the sarcomere and the nucleus in
RT skeletal muscle.";
RL J. Mol. Biol. 339:313-325(2004).
RN [12]
RP FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, AND INTERACTION WITH
RP ALYREF/THOC4; NCL; XRCC5; WRN AND MSH2.
RX PubMed=14718551; DOI=10.1093/nar/gkh170;
RA Gaudreault I., Guay D., Lebel M.;
RT "YB-1 promotes strand separation in vitro of duplex DNA containing
RT either mispaired bases or cisplatin modifications, exhibits
RT endonucleolytic activities and binds several DNA repair proteins.";
RL Nucleic Acids Res. 32:316-327(2004).
RN [13]
RP IDENTIFICATION IN A COMPLEX WITH THE U11/U12 SPLICEOSOME, AND MASS
RP SPECTROMETRY.
RX PubMed=15146077; DOI=10.1261/rna.7320604;
RA Will C.L., Schneider C., Hossbach M., Urlaub H., Rauhut R.,
RA Elbashir S., Tuschl T., Luehrmann R.;
RT "The human 18S U11/U12 snRNP contains a set of novel proteins not
RT found in the U2-dependent spliceosome.";
RL RNA 10:929-941(2004).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-162, AND MASS
RP SPECTROMETRY.
RX PubMed=15592455; DOI=10.1038/nbt1046;
RA Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H.,
RA Zha X.-M., Polakiewicz R.D., Comb M.J.;
RT "Immunoaffinity profiling of tyrosine phosphorylation in cancer
RT cells.";
RL Nat. Biotechnol. 23:94-101(2005).
RN [15]
RP PHOSPHORYLATION AT SER-102, INTERACTION WITH AKT1, SUBCELLULAR
RP LOCATION, AND MUTAGENESIS OF SER-102.
RX PubMed=15806160; DOI=10.1038/sj.onc.1208590;
RA Sutherland B.W., Kucab J., Wu J., Lee C., Cheang M.C.U., Yorida E.,
RA Turbin D., Dedhar S., Nelson C., Pollak M., Leighton Grimes H.,
RA Miller K., Badve S., Huntsman D., Blake-Gilks C., Chen M.,
RA Pallen C.J., Dunn S.E.;
RT "Akt phosphorylates the Y-box binding protein 1 at Ser102 located in
RT the cold shock domain and affects the anchorage-independent growth of
RT breast cancer cells.";
RL Oncogene 24:4281-4292(2005).
RN [16]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174 AND SER-176, AND
RP MASS SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=17081983; DOI=10.1016/j.cell.2006.09.026;
RA Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P.,
RA Mann M.;
RT "Global, in vivo, and site-specific phosphorylation dynamics in
RT signaling networks.";
RL Cell 127:635-648(2006).
RN [17]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=16964243; DOI=10.1038/nbt1240;
RA Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P.;
RT "A probability-based approach for high-throughput protein
RT phosphorylation analysis and site localization.";
RL Nat. Biotechnol. 24:1285-1292(2006).
RN [18]
RP INTERACTION WITH AGO1 AND AGO2.
RX PubMed=17932509; DOI=10.1038/sj.embor.7401088;
RA Hoeck J., Weinmann L., Ender C., Ruedel S., Kremmer E., Raabe M.,
RA Urlaub H., Meister G.;
RT "Proteomic and functional analysis of Argonaute-containing mRNA-
RT protein complexes in human cells.";
RL EMBO Rep. 8:1052-1060(2007).
RN [19]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Prostate cancer;
RX PubMed=17487921; DOI=10.1002/elps.200600782;
RA Giorgianni F., Zhao Y., Desiderio D.M., Beranova-Giorgianni S.;
RT "Toward a global characterization of the phosphoproteome in prostate
RT cancer cells: identification of phosphoproteins in the LNCaP cell
RT line.";
RL Electrophoresis 28:2027-2034(2007).
RN [20]
RP IDENTIFICATION IN A MRNP GRANULE COMPLEX, INTERACTION WITH IGF2BP1,
RP SUBCELLULAR LOCATION, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=17289661; DOI=10.1074/mcp.M600346-MCP200;
RA Joeson L., Vikesaa J., Krogh A., Nielsen L.K., Hansen T., Borup R.,
RA Johnsen A.H., Christiansen J., Nielsen F.C.;
RT "Molecular composition of IMP1 ribonucleoprotein granules.";
RL Mol. Cell. Proteomics 6:798-811(2007).
RN [21]
RP INTERACTION WITH RBBP6, AND UBIQUITINATION.
RX PubMed=18851979; DOI=10.1016/j.jmb.2008.09.060;
RA Chibi M., Meyer M., Skepu A., Rees D.J.G., Moolman-Smook J.C.,
RA Pugh D.J.;
RT "RBBP6 interacts with multifunctional protein YB-1 through its RING
RT finger domain, leading to ubiquitination and proteosomal degradation
RT of YB-1.";
RL J. Mol. Biol. 384:908-916(2008).
RN [22]
RP FUNCTION, INTERACTION WITH MBNL1, SUBCELLULAR LOCATION, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=18335541; DOI=10.1002/jnr.21655;
RA Onishi H., Kino Y., Morita T., Futai E., Sasagawa N., Ishiura S.;
RT "MBNL1 associates with YB-1 in cytoplasmic stress granules.";
RL J. Neurosci. Res. 86:1994-2002(2008).
RN [23]
RP FUNCTION, DNA-BINDING, AND INTERACTION WITH APEX1.
RX PubMed=18809583; DOI=10.1128/MCB.00244-08;
RA Chattopadhyay R., Das S., Maiti A.K., Boldogh I., Xie J., Hazra T.K.,
RA Kohno K., Mitra S., Bhakat K.K.;
RT "Regulatory role of human AP-endonuclease (APE1/Ref-1) in YB-1-
RT mediated activation of the multidrug resistance gene MDR1.";
RL Mol. Cell. Biol. 28:7066-7080(2008).
RN [24]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174 AND SER-176, AND
RP MASS SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [25]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,
RA Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in
RT a refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [26]
RP FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF LYS-301 AND LYS-304,
RP AND ACETYLATION AT LYS-301 AND LYS-304.
RX PubMed=19483673; DOI=10.1038/embor.2009.81;
RA Frye B.C., Halfter S., Djudjaj S., Muehlenberg P., Weber S.,
RA Raffetseder U., En-Nia A., Knott H., Baron J.M., Dooley S.,
RA Bernhagen J., Mertens P.R.;
RT "Y-box protein-1 is actively secreted through a non-classical pathway
RT and acts as an extracellular mitogen.";
RL EMBO Rep. 10:783-789(2009).
RN [27]
RP RNA-BINDING.
RX PubMed=19561594; DOI=10.1038/nbt.1550;
RA Ray D., Kazan H., Chan E.T., Pena Castillo L., Chaudhry S.,
RA Talukder S., Blencowe B.J., Morris Q., Hughes T.R.;
RT "Rapid and systematic analysis of the RNA recognition specificities of
RT RNA-binding proteins.";
RL Nat. Biotechnol. 27:667-670(2009).
RN [28]
RP FUNCTION, COMPONENT OF THE CRD-MEDIATED MRNA STABILIZATION COMPLEX,
RP IDENTIFICATION IN A MRNP COMPLEX, SUBCELLULAR LOCATION, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=19029303; DOI=10.1261/rna.1175909;
RA Weidensdorfer D., Stoehr N., Baude A., Lederer M., Koehn M.,
RA Schierhorn A., Buchmeier S., Wahle E., Huettelmaiery S.;
RT "Control of c-myc mRNA stability by IGF2BP1-associated cytoplasmic
RT RNPs.";
RL RNA 15:104-115(2009).
RN [29]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-102; SER-165; SER-167;
RP SER-174 AND SER-176, AND MASS SPECTROMETRY.
RC TISSUE=Leukemic T-cell;
RX PubMed=19690332; DOI=10.1126/scisignal.2000007;
RA Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
RA Rodionov V., Han D.K.;
RT "Quantitative phosphoproteomic analysis of T cell receptor signaling
RT reveals system-wide modulation of protein-protein interactions.";
RL Sci. Signal. 2:RA46-RA46(2009).
RN [30]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-165; SER-167; SER-174
RP AND SER-176, AND MASS SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
RA Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full
RT phosphorylation site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [31]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
RA Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [32]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-165; SER-167; SER-174;
RP SER-176 AND SER-314, AND MASS SPECTROMETRY.
RX PubMed=21406692; DOI=10.1126/scisignal.2001570;
RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
RA Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
RA Blagoev B.;
RT "System-wide temporal characterization of the proteome and
RT phosphoproteome of human embryonic stem cell differentiation.";
RL Sci. Signal. 4:RS3-RS3(2011).
RN [33]
RP STRUCTURE BY NMR OF 52-129, AND INTERACTION WITH SS-DNA.
RX PubMed=11851341; DOI=10.1006/jmbi.2001.5334;
RA Kloks C.P.A.M., Spronk C.A.E.M., Lasonder E., Hoffmann A.,
RA Vuister G.W., Grzesiek S., Hilbers C.W.;
RT "The solution structure and DNA-binding properties of the cold-shock
RT domain of the human Y-box protein YB-1.";
RL J. Mol. Biol. 316:317-326(2002).
CC -!- FUNCTION: Mediates pre-mRNA alternative splicing regulation. Binds
CC to splice sites in pre-mRNA and regulates splice site selection.
CC Binds and stabilizes cytoplasmic mRNA. Contributes to the
CC regulation of translation by modulating the interaction between
CC the mRNA and eukaryotic initiation factors (By similarity).
CC Regulates the transcription of numerous genes. Its transcriptional
CC activity on the multidrug resistance gene MDR1 is enhanced in
CC presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7'.
CC Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such
CC as MDR1 and HLA class II genes. Promotes separation of DNA strands
CC that contain mismatches or are modified by cisplatin. Has
CC endonucleolytic activity and can introduce nicks or breaks into
CC double-stranded DNA (in vitro). May play a role in DNA repair.
CC Component of the CRD-mediated complex that promotes MYC mRNA
CC stability. Binds preferentially to the 5'-[CU]CUGCG-3' motif in
CC vitro.
CC -!- FUNCTION: The secreted form acts as an extracellular mitogen and
CC stimulates cell migration and proliferation.
CC -!- SUBUNIT: Identified in a histone pre-mRNA complex, at least
CC composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (By
CC similarity). Component of the coding region determinant (CRD)-
CC mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and
CC YBX1. Identified in a IGF2BP1-dependent mRNP granule complex
CC containing untranslated mRNAs. Component of the U11/U12 snRNPs
CC that are part of the U12-type spliceosome. Interacts with IGF2BP1
CC and RBBP6. Component of cytoplasmic messenger ribonucleoprotein
CC particles (mRNPs). Interacts with AKT1, MBNL1, SFRS9,
CC ALYREF/THOC4, MSH2, XRCC5, WRN and NCL. Can bind to DNA as a
CC homomeric form, (EFI-A)n or as a heteromeric form in association
CC with EFI-B. Homodimer in the presence of ATP. Interacts (via C-
CC terminus) with APEX1 (via N-terminus); the interaction is
CC increased with APEX1 acetylated at 'Lys-6' and 'Lys-7'. Interacts
CC with AGO1 and AGO2. Interacts with ANKRD2.
CC -!- INTERACTION:
CC Q08705:CTCF (xeno); NbExp=2; IntAct=EBI-354065, EBI-932806;
CC Q08211:DHX9; NbExp=5; IntAct=EBI-354065, EBI-352022;
CC Q09472:EP300; NbExp=2; IntAct=EBI-354065, EBI-447295;
CC Q7Z6M2:FBXO33; NbExp=5; IntAct=EBI-354065, EBI-8555452;
CC Q14103-4:HNRNPD; NbExp=3; IntAct=EBI-354065, EBI-432545;
CC Q99697:PITX2; NbExp=3; IntAct=EBI-354065, EBI-1175211;
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Cytoplasmic granule.
CC Secreted. Note=Localized in cytoplasmic mRNP granules containing
CC untranslated mRNAs. Shuttles between nucleus and cytoplasm.
CC Predominantly cytoplasmic in proliferating cells. Cytotoxic stress
CC and DNA damage enhance translocation to the nucleus. Localized
CC with DDX1, MBNL1 and TIAL1 in stress granules upon stress.
CC Secreted by mesangial and monocytic cells after inflammatory
CC challenges. Translocates from the cytoplasm to the nucleus after
CC and colocalizes with APEX1 in nuclear speckles after genotoxic
CC stress.
CC -!- PTM: Ubiquitinated by RBBP6; leading to a decrease of YBX1
CC transcactivational ability.
CC -!- PTM: In the absence of phosphorylation the protein is retained in
CC the cytoplasm.
CC -!- PTM: Cleaved by a 20S proteasomal protease in response to agents
CC that damage DNA. Cleavage takes place in the absence of
CC ubiquitination and ATP. The resulting N-terminal fragment
CC accumulates in the nucleus (By similarity).
CC -!- SIMILARITY: Contains 1 CSD (cold-shock) domain.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA35750.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
CC Sequence=AAA59949.1; Type=Frameshift; Positions=Several;
CC Sequence=AAA61308.1; Type=Frameshift; Positions=314;
CC -!- WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology
CC and Haematology;
CC URL="http://atlasgeneticsoncology.org/Genes/YBX1ID46554ch1p34.html";
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DR EMBL; M24070; AAA35750.1; ALT_INIT; mRNA.
DR EMBL; J03827; AAA61308.1; ALT_FRAME; mRNA.
DR EMBL; M83234; AAA59949.1; ALT_FRAME; mRNA.
DR EMBL; L28809; AAA20871.1; -; mRNA.
DR EMBL; BC002411; AAH02411.1; -; mRNA.
DR EMBL; BC010430; AAH10430.1; -; mRNA.
DR EMBL; BC015208; AAH15208.1; -; mRNA.
DR EMBL; BC038384; AAH38384.1; -; mRNA.
DR EMBL; BC065571; AAH65571.1; -; mRNA.
DR EMBL; BC070084; AAH70084.1; -; mRNA.
DR EMBL; BC071708; AAH71708.1; -; mRNA.
DR EMBL; BC090038; AAH90038.1; -; mRNA.
DR EMBL; BC098435; AAH98435.1; -; mRNA.
DR EMBL; BC106045; AAI06046.1; -; mRNA.
DR PIR; I39382; I39382.
DR PIR; S34426; S34426.
DR RefSeq; NP_004550.2; NM_004559.3.
DR UniGene; Hs.473583; -.
DR PDB; 1H95; NMR; -; A=52-129.
DR PDBsum; 1H95; -.
DR ProteinModelPortal; P67809; -.
DR SMR; P67809; 52-129.
DR DIP; DIP-29405N; -.
DR IntAct; P67809; 134.
DR MINT; MINT-5001202; -.
DR STRING; 9606.ENSP00000361626; -.
DR PhosphoSite; P67809; -.
DR DMDM; 54040031; -.
DR PaxDb; P67809; -.
DR PRIDE; P67809; -.
DR DNASU; 4904; -.
DR Ensembl; ENST00000321358; ENSP00000361626; ENSG00000065978.
DR GeneID; 4904; -.
DR KEGG; hsa:4904; -.
DR UCSC; uc001chs.3; human.
DR CTD; 4904; -.
DR GeneCards; GC01P043148; -.
DR H-InvDB; HIX0037767; -.
DR H-InvDB; HIX0172381; -.
DR HGNC; HGNC:8014; YBX1.
DR HPA; CAB005875; -.
DR HPA; HPA040304; -.
DR MIM; 154030; gene.
DR neXtProt; NX_P67809; -.
DR PharmGKB; PA31791; -.
DR eggNOG; COG1278; -.
DR HOGENOM; HOG000116439; -.
DR HOVERGEN; HBG008757; -.
DR InParanoid; P67809; -.
DR KO; K09276; -.
DR OMA; ADRNRYR; -.
DR PhylomeDB; P67809; -.
DR Reactome; REACT_1675; mRNA Processing.
DR Reactome; REACT_71; Gene Expression.
DR SignaLink; P67809; -.
DR EvolutionaryTrace; P67809; -.
DR GeneWiki; Y_box_binding_protein_1; -.
DR GenomeRNAi; 4904; -.
DR NextBio; 18871; -.
DR PMAP-CutDB; P67809; -.
DR PRO; PR:P67809; -.
DR ArrayExpress; P67809; -.
DR Bgee; P67809; -.
DR CleanEx; HS_YBX1; -.
DR Genevestigator; P67809; -.
DR GO; GO:0070937; C:CRD-mediated mRNA stability complex; IDA:UniProtKB.
DR GO; GO:0010494; C:cytoplasmic stress granule; IDA:UniProtKB.
DR GO; GO:0070062; C:extracellular vesicular exosome; IDA:UniProtKB.
DR GO; GO:0071204; C:histone pre-mRNA 3'end processing complex; ISS:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005689; C:U12-type spliceosomal complex; IDA:UniProtKB.
DR GO; GO:0003690; F:double-stranded DNA binding; TAS:ProtInc.
DR GO; GO:0003723; F:RNA binding; IDA:UniProtKB.
DR GO; GO:0003700; F:sequence-specific DNA binding transcription factor activity; TAS:ProtInc.
DR GO; GO:0003697; F:single-stranded DNA binding; TAS:ProtInc.
DR GO; GO:0070934; P:CRD-mediated mRNA stabilization; IMP:UniProtKB.
DR GO; GO:0001701; P:in utero embryonic development; IEA:Ensembl.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; TAS:Reactome.
DR GO; GO:0051154; P:negative regulation of striated muscle cell differentiation; IEA:Ensembl.
DR GO; GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IEA:Ensembl.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-dependent; NAS:UniProtKB.
DR GO; GO:0051781; P:positive regulation of cell division; IEA:UniProtKB-KW.
DR GO; GO:0006366; P:transcription from RNA polymerase II promoter; TAS:ProtInc.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR019844; Cold-shock_CS.
DR InterPro; IPR011129; Cold_shock_prot.
DR InterPro; IPR002059; CSP_DNA-bd.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF00313; CSD; 1.
DR PRINTS; PR00050; COLDSHOCK.
DR SMART; SM00357; CSP; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR PROSITE; PS00352; COLD_SHOCK; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Activator; Complete proteome; Cytoplasm;
KW Direct protein sequencing; DNA-binding; Isopeptide bond; Mitogen;
KW mRNA processing; mRNA splicing; Nucleus; Phosphoprotein;
KW Reference proteome; Repressor; RNA-binding; Secreted; Transcription;
KW Transcription regulation; Ubl conjugation.
FT INIT_MET 1 1 Removed.
FT CHAIN 2 324 Nuclease-sensitive element-binding
FT protein 1.
FT /FTId=PRO_0000100219.
FT DOMAIN 61 125 CSD.
FT REGION 15 71 Interaction with ss-DNA.
FT SITE 219 220 Cleavage; by 20S proteasomal protease.
FT MOD_RES 2 2 N-acetylserine.
FT MOD_RES 102 102 Phosphoserine; by PKB/AKT1.
FT MOD_RES 162 162 Phosphotyrosine.
FT MOD_RES 165 165 Phosphoserine.
FT MOD_RES 167 167 Phosphoserine.
FT MOD_RES 174 174 Phosphoserine.
FT MOD_RES 176 176 Phosphoserine.
FT MOD_RES 301 301 N6-acetyllysine.
FT MOD_RES 304 304 N6-acetyllysine.
FT MOD_RES 314 314 Phosphoserine.
FT CROSSLNK 137 137 Glycyl lysine isopeptide (Lys-Gly)
FT (interchain with G-Cter in ubiquitin).
FT MUTAGEN 102 102 S->A: Loss of phosphorylation by
FT PKB/AKT1. Inhibits translocation to the
FT nucleus and tumor cell growth.
FT MUTAGEN 301 301 K->A: Abrogates unconventional secretion.
FT MUTAGEN 304 304 K->A: Abrogates unconventional secretion.
FT CONFLICT 120 120 A -> E (in Ref. 2; AAA61308).
FT STRAND 56 67
FT TURN 68 71
FT STRAND 72 77
FT TURN 78 81
FT STRAND 82 87
FT HELIX 88 90
FT STRAND 108 115
FT STRAND 117 125
SQ SEQUENCE 324 AA; 35924 MW; DF0114BF974AEDB8 CRC64;
MSSEAETQQP PAAPPAAPAL SAADTKPGTT GSGAGSGGPG GLTSAAPAGG DKKVIATKVL
GTVKWFNVRN GYGFINRNDT KEDVFVHQTA IKKNNPRKYL RSVGDGETVE FDVVEGEKGA
EAANVTGPGG VPVQGSKYAA DRNHYRRYPR RRGPPRNYQQ NYQNSESGEK NEGSESAPEG
QAQQRRPYRR RRFPPYYMRR PYGRRPQYSN PPVQGEVMEG ADNQGAGEQG RPVRQNMYRG
YRPRFRRGPP RQRQPREDGN EEDKENQGDE TQGQQPPQRR YRRNFNYRRR RPENPKPQDG
KETKAADPPA ENSSAPEAEQ GGAE
//
ID YBOX1_HUMAN Reviewed; 324 AA.
AC P67809; P16990; P16991; Q14972; Q15325; Q5FVF0;
DT 11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
read moreDT 23-JAN-2007, sequence version 3.
DT 22-JAN-2014, entry version 116.
DE RecName: Full=Nuclease-sensitive element-binding protein 1;
DE AltName: Full=CCAAT-binding transcription factor I subunit A;
DE Short=CBF-A;
DE AltName: Full=DNA-binding protein B;
DE Short=DBPB;
DE AltName: Full=Enhancer factor I subunit A;
DE Short=EFI-A;
DE AltName: Full=Y-box transcription factor;
DE AltName: Full=Y-box-binding protein 1;
DE Short=YB-1;
GN Name=YBX1; Synonyms=NSEP1, YB1;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=2977358; DOI=10.1016/0378-1119(88)90514-8;
RA Sakura H., Maekawa T., Imamoto F., Yasuda K., Ishii S.;
RT "Two human genes isolated by a novel method encode DNA-binding
RT proteins containing a common region of homology.";
RL Gene 73:499-507(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=3174636; DOI=10.1073/pnas.85.19.7322;
RA Didier D.K., Schiffenbauer J., Woulfe S.L., Zacheis M., Schwartz B.D.;
RT "Characterization of the cDNA encoding a protein binding to the major
RT histocompatibility complex class II Y box.";
RL Proc. Natl. Acad. Sci. U.S.A. 85:7322-7326(1988).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=1891370; DOI=10.1093/nar/19.17.4771;
RA Kolluri R., Kinniburgh A.J.;
RT "Full length cDNA sequence encoding a nuclease-sensitive element DNA
RT binding protein.";
RL Nucleic Acids Res. 19:4771-4771(1991).
RN [4]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Bone marrow;
RX PubMed=8188694;
RA Horwitz E.M., Maloney K.A., Ley T.J.;
RT "A human protein containing a 'cold shock' domain binds specifically
RT to H-DNA upstream from the human gamma-globin genes.";
RL J. Biol. Chem. 269:14130-14139(1994).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Adrenal cortex, Eye, Kidney, Muscle, Placenta, Skin, Testis,
RC and Uterus;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [6]
RP PROTEIN SEQUENCE OF 2-53; 70-93; 102-137; 157-185; 205-231; 257-279
RP AND 305-324, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2,
RP PHOSPHORYLATION AT SER-165, AND MASS SPECTROMETRY.
RC TISSUE=Ovarian carcinoma;
RA Bienvenut W.V.;
RL Submitted (JAN-2010) to UniProtKB.
RN [7]
RP FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
RX PubMed=10817758;
RA Chen C.-Y., Gherzi R., Andersen J.S., Gaietta G., Juerchott K.,
RA Royer H.-D., Mann M., Karin M.;
RT "Nucleolin and YB-1 are required for JNK-mediated interleukin-2 mRNA
RT stabilization during T-cell activation.";
RL Genes Dev. 14:1236-1248(2000).
RN [8]
RP FUNCTION.
RX PubMed=11698476;
RA Capowski E.E., Esnault S., Bhattacharya S., Malter J.S.;
RT "Y box-binding factor promotes eosinophil survival by stabilizing
RT granulocyte-macrophage colony-stimulating factor mRNA.";
RL J. Immunol. 167:5970-5976(2001).
RN [9]
RP FUNCTION, INTERACTION WITH SFRS9, AND SUBCELLULAR LOCATION.
RX PubMed=12604611; DOI=10.1074/jbc.M212518200;
RA Raffetseder U., Frye B., Rauen T., Juerchott K., Royer H.-D.,
RA Jansen P.L., Mertens P.R.;
RT "Splicing factor SRp30c interaction with Y-box protein-1 confers
RT nuclear YB-1 shuttling and alternative splice site selection.";
RL J. Biol. Chem. 278:18241-18248(2003).
RN [10]
RP INTERACTION WITH SFRS12.
RX PubMed=14559993; DOI=10.1128/MCB.23.21.7437-7447.2003;
RA Li J., Hawkins I.C., Harvey C.D., Jennings J.L., Link A.J.,
RA Patton J.G.;
RT "Regulation of alternative splicing by SRrp86 and its interacting
RT proteins.";
RL Mol. Cell. Biol. 23:7437-7447(2003).
RN [11]
RP INTERACTION WITH ANKRD2.
RX PubMed=15136035; DOI=10.1016/j.jmb.2004.03.071;
RA Kojic S., Medeot E., Guccione E., Krmac H., Zara I., Martinelli V.,
RA Valle G., Faulkner G.;
RT "The Ankrd2 protein, a link between the sarcomere and the nucleus in
RT skeletal muscle.";
RL J. Mol. Biol. 339:313-325(2004).
RN [12]
RP FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, AND INTERACTION WITH
RP ALYREF/THOC4; NCL; XRCC5; WRN AND MSH2.
RX PubMed=14718551; DOI=10.1093/nar/gkh170;
RA Gaudreault I., Guay D., Lebel M.;
RT "YB-1 promotes strand separation in vitro of duplex DNA containing
RT either mispaired bases or cisplatin modifications, exhibits
RT endonucleolytic activities and binds several DNA repair proteins.";
RL Nucleic Acids Res. 32:316-327(2004).
RN [13]
RP IDENTIFICATION IN A COMPLEX WITH THE U11/U12 SPLICEOSOME, AND MASS
RP SPECTROMETRY.
RX PubMed=15146077; DOI=10.1261/rna.7320604;
RA Will C.L., Schneider C., Hossbach M., Urlaub H., Rauhut R.,
RA Elbashir S., Tuschl T., Luehrmann R.;
RT "The human 18S U11/U12 snRNP contains a set of novel proteins not
RT found in the U2-dependent spliceosome.";
RL RNA 10:929-941(2004).
RN [14]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-162, AND MASS
RP SPECTROMETRY.
RX PubMed=15592455; DOI=10.1038/nbt1046;
RA Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H.,
RA Zha X.-M., Polakiewicz R.D., Comb M.J.;
RT "Immunoaffinity profiling of tyrosine phosphorylation in cancer
RT cells.";
RL Nat. Biotechnol. 23:94-101(2005).
RN [15]
RP PHOSPHORYLATION AT SER-102, INTERACTION WITH AKT1, SUBCELLULAR
RP LOCATION, AND MUTAGENESIS OF SER-102.
RX PubMed=15806160; DOI=10.1038/sj.onc.1208590;
RA Sutherland B.W., Kucab J., Wu J., Lee C., Cheang M.C.U., Yorida E.,
RA Turbin D., Dedhar S., Nelson C., Pollak M., Leighton Grimes H.,
RA Miller K., Badve S., Huntsman D., Blake-Gilks C., Chen M.,
RA Pallen C.J., Dunn S.E.;
RT "Akt phosphorylates the Y-box binding protein 1 at Ser102 located in
RT the cold shock domain and affects the anchorage-independent growth of
RT breast cancer cells.";
RL Oncogene 24:4281-4292(2005).
RN [16]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174 AND SER-176, AND
RP MASS SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=17081983; DOI=10.1016/j.cell.2006.09.026;
RA Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P.,
RA Mann M.;
RT "Global, in vivo, and site-specific phosphorylation dynamics in
RT signaling networks.";
RL Cell 127:635-648(2006).
RN [17]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=16964243; DOI=10.1038/nbt1240;
RA Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P.;
RT "A probability-based approach for high-throughput protein
RT phosphorylation analysis and site localization.";
RL Nat. Biotechnol. 24:1285-1292(2006).
RN [18]
RP INTERACTION WITH AGO1 AND AGO2.
RX PubMed=17932509; DOI=10.1038/sj.embor.7401088;
RA Hoeck J., Weinmann L., Ender C., Ruedel S., Kremmer E., Raabe M.,
RA Urlaub H., Meister G.;
RT "Proteomic and functional analysis of Argonaute-containing mRNA-
RT protein complexes in human cells.";
RL EMBO Rep. 8:1052-1060(2007).
RN [19]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Prostate cancer;
RX PubMed=17487921; DOI=10.1002/elps.200600782;
RA Giorgianni F., Zhao Y., Desiderio D.M., Beranova-Giorgianni S.;
RT "Toward a global characterization of the phosphoproteome in prostate
RT cancer cells: identification of phosphoproteins in the LNCaP cell
RT line.";
RL Electrophoresis 28:2027-2034(2007).
RN [20]
RP IDENTIFICATION IN A MRNP GRANULE COMPLEX, INTERACTION WITH IGF2BP1,
RP SUBCELLULAR LOCATION, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=17289661; DOI=10.1074/mcp.M600346-MCP200;
RA Joeson L., Vikesaa J., Krogh A., Nielsen L.K., Hansen T., Borup R.,
RA Johnsen A.H., Christiansen J., Nielsen F.C.;
RT "Molecular composition of IMP1 ribonucleoprotein granules.";
RL Mol. Cell. Proteomics 6:798-811(2007).
RN [21]
RP INTERACTION WITH RBBP6, AND UBIQUITINATION.
RX PubMed=18851979; DOI=10.1016/j.jmb.2008.09.060;
RA Chibi M., Meyer M., Skepu A., Rees D.J.G., Moolman-Smook J.C.,
RA Pugh D.J.;
RT "RBBP6 interacts with multifunctional protein YB-1 through its RING
RT finger domain, leading to ubiquitination and proteosomal degradation
RT of YB-1.";
RL J. Mol. Biol. 384:908-916(2008).
RN [22]
RP FUNCTION, INTERACTION WITH MBNL1, SUBCELLULAR LOCATION, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=18335541; DOI=10.1002/jnr.21655;
RA Onishi H., Kino Y., Morita T., Futai E., Sasagawa N., Ishiura S.;
RT "MBNL1 associates with YB-1 in cytoplasmic stress granules.";
RL J. Neurosci. Res. 86:1994-2002(2008).
RN [23]
RP FUNCTION, DNA-BINDING, AND INTERACTION WITH APEX1.
RX PubMed=18809583; DOI=10.1128/MCB.00244-08;
RA Chattopadhyay R., Das S., Maiti A.K., Boldogh I., Xie J., Hazra T.K.,
RA Kohno K., Mitra S., Bhakat K.K.;
RT "Regulatory role of human AP-endonuclease (APE1/Ref-1) in YB-1-
RT mediated activation of the multidrug resistance gene MDR1.";
RL Mol. Cell. Biol. 28:7066-7080(2008).
RN [24]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174 AND SER-176, AND
RP MASS SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [25]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,
RA Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in
RT a refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [26]
RP FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF LYS-301 AND LYS-304,
RP AND ACETYLATION AT LYS-301 AND LYS-304.
RX PubMed=19483673; DOI=10.1038/embor.2009.81;
RA Frye B.C., Halfter S., Djudjaj S., Muehlenberg P., Weber S.,
RA Raffetseder U., En-Nia A., Knott H., Baron J.M., Dooley S.,
RA Bernhagen J., Mertens P.R.;
RT "Y-box protein-1 is actively secreted through a non-classical pathway
RT and acts as an extracellular mitogen.";
RL EMBO Rep. 10:783-789(2009).
RN [27]
RP RNA-BINDING.
RX PubMed=19561594; DOI=10.1038/nbt.1550;
RA Ray D., Kazan H., Chan E.T., Pena Castillo L., Chaudhry S.,
RA Talukder S., Blencowe B.J., Morris Q., Hughes T.R.;
RT "Rapid and systematic analysis of the RNA recognition specificities of
RT RNA-binding proteins.";
RL Nat. Biotechnol. 27:667-670(2009).
RN [28]
RP FUNCTION, COMPONENT OF THE CRD-MEDIATED MRNA STABILIZATION COMPLEX,
RP IDENTIFICATION IN A MRNP COMPLEX, SUBCELLULAR LOCATION, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=19029303; DOI=10.1261/rna.1175909;
RA Weidensdorfer D., Stoehr N., Baude A., Lederer M., Koehn M.,
RA Schierhorn A., Buchmeier S., Wahle E., Huettelmaiery S.;
RT "Control of c-myc mRNA stability by IGF2BP1-associated cytoplasmic
RT RNPs.";
RL RNA 15:104-115(2009).
RN [29]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-102; SER-165; SER-167;
RP SER-174 AND SER-176, AND MASS SPECTROMETRY.
RC TISSUE=Leukemic T-cell;
RX PubMed=19690332; DOI=10.1126/scisignal.2000007;
RA Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
RA Rodionov V., Han D.K.;
RT "Quantitative phosphoproteomic analysis of T cell receptor signaling
RT reveals system-wide modulation of protein-protein interactions.";
RL Sci. Signal. 2:RA46-RA46(2009).
RN [30]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-165; SER-167; SER-174
RP AND SER-176, AND MASS SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
RA Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full
RT phosphorylation site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [31]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
RA Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [32]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-165; SER-167; SER-174;
RP SER-176 AND SER-314, AND MASS SPECTROMETRY.
RX PubMed=21406692; DOI=10.1126/scisignal.2001570;
RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
RA Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
RA Blagoev B.;
RT "System-wide temporal characterization of the proteome and
RT phosphoproteome of human embryonic stem cell differentiation.";
RL Sci. Signal. 4:RS3-RS3(2011).
RN [33]
RP STRUCTURE BY NMR OF 52-129, AND INTERACTION WITH SS-DNA.
RX PubMed=11851341; DOI=10.1006/jmbi.2001.5334;
RA Kloks C.P.A.M., Spronk C.A.E.M., Lasonder E., Hoffmann A.,
RA Vuister G.W., Grzesiek S., Hilbers C.W.;
RT "The solution structure and DNA-binding properties of the cold-shock
RT domain of the human Y-box protein YB-1.";
RL J. Mol. Biol. 316:317-326(2002).
CC -!- FUNCTION: Mediates pre-mRNA alternative splicing regulation. Binds
CC to splice sites in pre-mRNA and regulates splice site selection.
CC Binds and stabilizes cytoplasmic mRNA. Contributes to the
CC regulation of translation by modulating the interaction between
CC the mRNA and eukaryotic initiation factors (By similarity).
CC Regulates the transcription of numerous genes. Its transcriptional
CC activity on the multidrug resistance gene MDR1 is enhanced in
CC presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7'.
CC Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such
CC as MDR1 and HLA class II genes. Promotes separation of DNA strands
CC that contain mismatches or are modified by cisplatin. Has
CC endonucleolytic activity and can introduce nicks or breaks into
CC double-stranded DNA (in vitro). May play a role in DNA repair.
CC Component of the CRD-mediated complex that promotes MYC mRNA
CC stability. Binds preferentially to the 5'-[CU]CUGCG-3' motif in
CC vitro.
CC -!- FUNCTION: The secreted form acts as an extracellular mitogen and
CC stimulates cell migration and proliferation.
CC -!- SUBUNIT: Identified in a histone pre-mRNA complex, at least
CC composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (By
CC similarity). Component of the coding region determinant (CRD)-
CC mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and
CC YBX1. Identified in a IGF2BP1-dependent mRNP granule complex
CC containing untranslated mRNAs. Component of the U11/U12 snRNPs
CC that are part of the U12-type spliceosome. Interacts with IGF2BP1
CC and RBBP6. Component of cytoplasmic messenger ribonucleoprotein
CC particles (mRNPs). Interacts with AKT1, MBNL1, SFRS9,
CC ALYREF/THOC4, MSH2, XRCC5, WRN and NCL. Can bind to DNA as a
CC homomeric form, (EFI-A)n or as a heteromeric form in association
CC with EFI-B. Homodimer in the presence of ATP. Interacts (via C-
CC terminus) with APEX1 (via N-terminus); the interaction is
CC increased with APEX1 acetylated at 'Lys-6' and 'Lys-7'. Interacts
CC with AGO1 and AGO2. Interacts with ANKRD2.
CC -!- INTERACTION:
CC Q08705:CTCF (xeno); NbExp=2; IntAct=EBI-354065, EBI-932806;
CC Q08211:DHX9; NbExp=5; IntAct=EBI-354065, EBI-352022;
CC Q09472:EP300; NbExp=2; IntAct=EBI-354065, EBI-447295;
CC Q7Z6M2:FBXO33; NbExp=5; IntAct=EBI-354065, EBI-8555452;
CC Q14103-4:HNRNPD; NbExp=3; IntAct=EBI-354065, EBI-432545;
CC Q99697:PITX2; NbExp=3; IntAct=EBI-354065, EBI-1175211;
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Cytoplasmic granule.
CC Secreted. Note=Localized in cytoplasmic mRNP granules containing
CC untranslated mRNAs. Shuttles between nucleus and cytoplasm.
CC Predominantly cytoplasmic in proliferating cells. Cytotoxic stress
CC and DNA damage enhance translocation to the nucleus. Localized
CC with DDX1, MBNL1 and TIAL1 in stress granules upon stress.
CC Secreted by mesangial and monocytic cells after inflammatory
CC challenges. Translocates from the cytoplasm to the nucleus after
CC and colocalizes with APEX1 in nuclear speckles after genotoxic
CC stress.
CC -!- PTM: Ubiquitinated by RBBP6; leading to a decrease of YBX1
CC transcactivational ability.
CC -!- PTM: In the absence of phosphorylation the protein is retained in
CC the cytoplasm.
CC -!- PTM: Cleaved by a 20S proteasomal protease in response to agents
CC that damage DNA. Cleavage takes place in the absence of
CC ubiquitination and ATP. The resulting N-terminal fragment
CC accumulates in the nucleus (By similarity).
CC -!- SIMILARITY: Contains 1 CSD (cold-shock) domain.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA35750.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
CC Sequence=AAA59949.1; Type=Frameshift; Positions=Several;
CC Sequence=AAA61308.1; Type=Frameshift; Positions=314;
CC -!- WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology
CC and Haematology;
CC URL="http://atlasgeneticsoncology.org/Genes/YBX1ID46554ch1p34.html";
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DR EMBL; M24070; AAA35750.1; ALT_INIT; mRNA.
DR EMBL; J03827; AAA61308.1; ALT_FRAME; mRNA.
DR EMBL; M83234; AAA59949.1; ALT_FRAME; mRNA.
DR EMBL; L28809; AAA20871.1; -; mRNA.
DR EMBL; BC002411; AAH02411.1; -; mRNA.
DR EMBL; BC010430; AAH10430.1; -; mRNA.
DR EMBL; BC015208; AAH15208.1; -; mRNA.
DR EMBL; BC038384; AAH38384.1; -; mRNA.
DR EMBL; BC065571; AAH65571.1; -; mRNA.
DR EMBL; BC070084; AAH70084.1; -; mRNA.
DR EMBL; BC071708; AAH71708.1; -; mRNA.
DR EMBL; BC090038; AAH90038.1; -; mRNA.
DR EMBL; BC098435; AAH98435.1; -; mRNA.
DR EMBL; BC106045; AAI06046.1; -; mRNA.
DR PIR; I39382; I39382.
DR PIR; S34426; S34426.
DR RefSeq; NP_004550.2; NM_004559.3.
DR UniGene; Hs.473583; -.
DR PDB; 1H95; NMR; -; A=52-129.
DR PDBsum; 1H95; -.
DR ProteinModelPortal; P67809; -.
DR SMR; P67809; 52-129.
DR DIP; DIP-29405N; -.
DR IntAct; P67809; 134.
DR MINT; MINT-5001202; -.
DR STRING; 9606.ENSP00000361626; -.
DR PhosphoSite; P67809; -.
DR DMDM; 54040031; -.
DR PaxDb; P67809; -.
DR PRIDE; P67809; -.
DR DNASU; 4904; -.
DR Ensembl; ENST00000321358; ENSP00000361626; ENSG00000065978.
DR GeneID; 4904; -.
DR KEGG; hsa:4904; -.
DR UCSC; uc001chs.3; human.
DR CTD; 4904; -.
DR GeneCards; GC01P043148; -.
DR H-InvDB; HIX0037767; -.
DR H-InvDB; HIX0172381; -.
DR HGNC; HGNC:8014; YBX1.
DR HPA; CAB005875; -.
DR HPA; HPA040304; -.
DR MIM; 154030; gene.
DR neXtProt; NX_P67809; -.
DR PharmGKB; PA31791; -.
DR eggNOG; COG1278; -.
DR HOGENOM; HOG000116439; -.
DR HOVERGEN; HBG008757; -.
DR InParanoid; P67809; -.
DR KO; K09276; -.
DR OMA; ADRNRYR; -.
DR PhylomeDB; P67809; -.
DR Reactome; REACT_1675; mRNA Processing.
DR Reactome; REACT_71; Gene Expression.
DR SignaLink; P67809; -.
DR EvolutionaryTrace; P67809; -.
DR GeneWiki; Y_box_binding_protein_1; -.
DR GenomeRNAi; 4904; -.
DR NextBio; 18871; -.
DR PMAP-CutDB; P67809; -.
DR PRO; PR:P67809; -.
DR ArrayExpress; P67809; -.
DR Bgee; P67809; -.
DR CleanEx; HS_YBX1; -.
DR Genevestigator; P67809; -.
DR GO; GO:0070937; C:CRD-mediated mRNA stability complex; IDA:UniProtKB.
DR GO; GO:0010494; C:cytoplasmic stress granule; IDA:UniProtKB.
DR GO; GO:0070062; C:extracellular vesicular exosome; IDA:UniProtKB.
DR GO; GO:0071204; C:histone pre-mRNA 3'end processing complex; ISS:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005689; C:U12-type spliceosomal complex; IDA:UniProtKB.
DR GO; GO:0003690; F:double-stranded DNA binding; TAS:ProtInc.
DR GO; GO:0003723; F:RNA binding; IDA:UniProtKB.
DR GO; GO:0003700; F:sequence-specific DNA binding transcription factor activity; TAS:ProtInc.
DR GO; GO:0003697; F:single-stranded DNA binding; TAS:ProtInc.
DR GO; GO:0070934; P:CRD-mediated mRNA stabilization; IMP:UniProtKB.
DR GO; GO:0001701; P:in utero embryonic development; IEA:Ensembl.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; TAS:Reactome.
DR GO; GO:0051154; P:negative regulation of striated muscle cell differentiation; IEA:Ensembl.
DR GO; GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IEA:Ensembl.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-dependent; NAS:UniProtKB.
DR GO; GO:0051781; P:positive regulation of cell division; IEA:UniProtKB-KW.
DR GO; GO:0006366; P:transcription from RNA polymerase II promoter; TAS:ProtInc.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR019844; Cold-shock_CS.
DR InterPro; IPR011129; Cold_shock_prot.
DR InterPro; IPR002059; CSP_DNA-bd.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF00313; CSD; 1.
DR PRINTS; PR00050; COLDSHOCK.
DR SMART; SM00357; CSP; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR PROSITE; PS00352; COLD_SHOCK; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Activator; Complete proteome; Cytoplasm;
KW Direct protein sequencing; DNA-binding; Isopeptide bond; Mitogen;
KW mRNA processing; mRNA splicing; Nucleus; Phosphoprotein;
KW Reference proteome; Repressor; RNA-binding; Secreted; Transcription;
KW Transcription regulation; Ubl conjugation.
FT INIT_MET 1 1 Removed.
FT CHAIN 2 324 Nuclease-sensitive element-binding
FT protein 1.
FT /FTId=PRO_0000100219.
FT DOMAIN 61 125 CSD.
FT REGION 15 71 Interaction with ss-DNA.
FT SITE 219 220 Cleavage; by 20S proteasomal protease.
FT MOD_RES 2 2 N-acetylserine.
FT MOD_RES 102 102 Phosphoserine; by PKB/AKT1.
FT MOD_RES 162 162 Phosphotyrosine.
FT MOD_RES 165 165 Phosphoserine.
FT MOD_RES 167 167 Phosphoserine.
FT MOD_RES 174 174 Phosphoserine.
FT MOD_RES 176 176 Phosphoserine.
FT MOD_RES 301 301 N6-acetyllysine.
FT MOD_RES 304 304 N6-acetyllysine.
FT MOD_RES 314 314 Phosphoserine.
FT CROSSLNK 137 137 Glycyl lysine isopeptide (Lys-Gly)
FT (interchain with G-Cter in ubiquitin).
FT MUTAGEN 102 102 S->A: Loss of phosphorylation by
FT PKB/AKT1. Inhibits translocation to the
FT nucleus and tumor cell growth.
FT MUTAGEN 301 301 K->A: Abrogates unconventional secretion.
FT MUTAGEN 304 304 K->A: Abrogates unconventional secretion.
FT CONFLICT 120 120 A -> E (in Ref. 2; AAA61308).
FT STRAND 56 67
FT TURN 68 71
FT STRAND 72 77
FT TURN 78 81
FT STRAND 82 87
FT HELIX 88 90
FT STRAND 108 115
FT STRAND 117 125
SQ SEQUENCE 324 AA; 35924 MW; DF0114BF974AEDB8 CRC64;
MSSEAETQQP PAAPPAAPAL SAADTKPGTT GSGAGSGGPG GLTSAAPAGG DKKVIATKVL
GTVKWFNVRN GYGFINRNDT KEDVFVHQTA IKKNNPRKYL RSVGDGETVE FDVVEGEKGA
EAANVTGPGG VPVQGSKYAA DRNHYRRYPR RRGPPRNYQQ NYQNSESGEK NEGSESAPEG
QAQQRRPYRR RRFPPYYMRR PYGRRPQYSN PPVQGEVMEG ADNQGAGEQG RPVRQNMYRG
YRPRFRRGPP RQRQPREDGN EEDKENQGDE TQGQQPPQRR YRRNFNYRRR RPENPKPQDG
KETKAADPPA ENSSAPEAEQ GGAE
//
MIM
154030
*RECORD*
*FIELD* NO
154030
*FIELD* TI
*154030 NUCLEASE-SENSITIVE ELEMENT-BINDING PROTEIN 1; NSEP1
;;MAJOR HISTOCOMPATIBILITY COMPLEX, CLASS II, Y BOX-BINDING PROTEIN
read more1; YB1;;
YBX1;;
DNA-BINDING PROTEIN B; DBPB
*FIELD* TX
CLONING
The expression of HLA class II genes is regulated by a series of
cis-acting elements and transacting factors. Several cis-acting elements
have been identified and have been termed the Z box, X box, Y box,
octamer, and TATA box. The Y box contains an inverted CCAAT box. Didier
et al. (1988) isolated a cDNA encoding a Y box-binding protein
designated YB1, or NSEP1. YB1 binding has an absolute requirement for
the CCAAT box and relative specificity for the Y box. It has a molecular
mass of 35,414 and contains 18% basic residues and putative nuclear
localization signals. Didier et al. (1988) found an inverse correlation
of YB1 and HLA-DR(beta) mRNA levels, suggesting that YB1 is a negative
regulatory factor.
By screening a human placenta cDNA expression library with DNA fragments
containing either the human epidermal growth factor receptor (EGFR;
131550) enhancer or the human c-erbB2 (164870) promoter, Sakura et al.
(1988) isolated cDNAs encoding DBPA (603437) and DBPB (NSEP1). The
deduced DBPA and DBPB proteins share a central region in which 100 of
109 amino acids are identical between the 2 proteins. Northern blot
analysis of HeLa cell RNA detected a 2.3-kb DBPB transcript.
Spitkovsky et al. (1992) cloned cDNAs encoding YB1 by screening a HeLa
cell cDNA expression library with an oligonucleotide containing a YB1
recognition site from the human papillomavirus type 18 enhancer. They
stated that the sequences of their cDNAs are identical to the sequence
of DBPB (Sakura et al., 1988) and nearly identical to the sequence of
the YB1 cDNA isolated by Didier et al. (1988). Northern blot analysis of
RNAs from a 24-week-old human fetus showed differential expression of
the YB1 gene. Immunoblot analysis of HeLa cell and fibroblast extracts
using antibodies against a YB1 synthetic peptide identified a 42-kD
nuclear protein.
Using an oligonucleotide containing the NSE of the MYC gene (190080)
gene as probe, Kolluri and Kinniburgh (1991) cloned NSEP1 from a HeLa
cell cDNA expression library. The deduced 322-amino acid protein
contains 4 putative DNA-binding domains, 3 of which are rich in basic
amino acids. Two of these basic regions, basic-1 and basic-2, form the
double-strand DNA-binding domain of the protein. NSEP1 also has a
pro/ser/thr-rich domain and an asp/glu/gln-rich domain, both of which
are reminiscent of activation domains. It also contains an octapeptide
single-strand DNA-binding motif that shares weak homology with the
ribonucleoprotein consensus sequence of RNA-binding proteins.
Kudo et al. (1995) isolated human cDNAs encoding DBPA and DBPB by
screening for proteins that bind to the human leukosialin (182160)
promoter. Northern blot analysis of human tissues detected the highest
DBPB expression levels in skeletal muscle and heart. The authors
isolated several DBPB processed pseudogenes and determined that they map
to many different chromosomes.
Coles et al. (1996) isolated human DBPA and DBPB cDNAs by screening for
proteins that are able to bind to the repressor element in the human
GMCSF (138960) promoter. The deduced 324-amino acid DBPB protein
contains a central cold-shock domain (CSD), which is a highly conserved,
approximately 100-amino acid domain with similarity to bacterial
cold-shock proteins. Overexpression of DBPB led to repression of the
GMCSF promoter.
GENE FUNCTION
Fukada and Tonks (2003) found that overexpression of Yb1 in Rat1 cells
resulted in increased Ptp1b (176885) expression. Depletion of Yb1
decreased Ptp1b expression, increased sensitivity to insulin, and
enhanced signaling through the cytokine receptor gp130 (IL6ST; 600694),
which was suppressed by reexpression of Ptp1b. Fukada and Tonks (2003)
also found a correlation between expression of PTP1B and YB1 in several
human cancer cell lines and in an animal model of type II diabetes (see
125853). They concluded that YB1 is an important regulator of PTP1B
expression.
Bhullar and Sollars (2011) found that Ybx1 was highly expressed in mouse
erythroid myeloid lymphoid clone-1 (EML), a hematopoietic precursor cell
line, but that it was downregulated in myeloid progenitors and in
Gmcsf-treated EML cells during myeloid differentiation.
Lineage-negative/Il7R (146661)-negative/Kit
(164920)-positive/Sca1-positive cells and
lineage-negative/Il7r-negative/Kit-positive/Sca1-negative cells
expressed high Ybx1 levels compared with differentiated cells, such as
granulocytes, in mouse bone marrow. Ybx1 was expressed at high levels in
myeloid leukemic cells at different developmental stages. Knockdown of
YBX1 in a human leukemic cell line inhibited proliferation ability,
induced apoptosis, and induced megakaryocytic differentiation in
response to arsenic trioxide treatment. Bhullar and Sollars (2011)
concluded that YBX1 is downregulated during myeloid differentiation and
that aberrant YBX1 expression in leukemic cells may contribute to
leukemia development by blocking differentiation.
GENE STRUCTURE
Makino et al. (1996) determined the nucleotide sequence of the first
exon and of 2,000 upstream nucleotides of the YB1 gene. The first exon
is unusually large and contains 166-bp coding sequence and a 331-bp
untranslated region. The GC content around the first exon is
approximately 70% and a CpG-free region was located in the untranslated
sequence. The segment preceding the major transcription initiation site
does not contain a TATA box, CCAAT box, or binding sequence for known
transcription factors. A transient expression assay using the
chloramphenicol acetyltransferase (CAT) gene showed that the sequence
from +24 to +281 was critical for CAT expression. PCR analysis on other
genomic phage DNAs showed that several clones were derived from
pseudogenes.
MAPPING
Kudo et al. (1995) mapped the human NSEP1 gene to 1p34-p33 using in situ
hybridization. By fluorescence in situ hybridization, Makino et al.
(1996) mapped the NSEP1 gene to 1p34.
*FIELD* RF
1. Bhullar, J.; Sollars, V. E.: YBX1 expression and function in early
hematopoiesis and leukemic cells. Immunogenetics 63: 337-350, 2011.
2. Coles, L. S.; Diamond, P.; Occhiodoro, F.; Vadas, M. A.; Shannon,
M. F.: Cold shock domain proteins repress transcription from the
GM-CSF promoter. Nucleic Acids Res. 24: 2311-2317, 1996.
3. Didier, D. K.; Schiffenbauer, J.; Woulfe, S. L.; Zacheis, M.; Schwartz,
B. D.: Characterization of the cDNA encoding a protein binding to
the major histocompatibility complex class II Y box. Proc. Nat. Acad.
Sci. 85: 7322-7326, 1988.
4. Fukada, T.; Tonks, N. K.: Identification of YB-1 as a regulator
of PTP1B expression: implications for regulation of insulin and cytokine
signaling. EMBO J. 22: 479-493, 2003.
5. Kolluri, R.; Kinniburgh, A. J.: Full length cDNA sequence encoding
a nuclease-sensitive element DNA binding protein. Nucleic Acids Res. 19:
4771 only, 1991.
6. Kudo, S.; Mattei, M.-G.; Fukuda, M.: Characterization of the gene
for dbpA, a family member of the nucleic-acid-binding proteins containing
a cold-shock domain. Europ. J. Biochem. 231: 72-82, 1995.
7. Makino, Y.; Ohga, T.; Toh, S.; Koike, K.; Okumura, K.; Wada, M.;
Kuwano, M.; Kohno, K.: Structural and functional analysis of the
human Y-box binding protein (YB-1) gene promoter. Nucleic Acid Res. 24:
1873-1878, 1996.
8. Sakura, H.; Maekawa, T.; Imamoto, F.; Yasuda, K.; Ishii, S.: Two
human genes isolated by a novel method encode DNA-binding proteins
containing a common region of homology. Gene 73: 499-507, 1988.
9. Spitkovsky, D. D.; Royer-Pokora, B.; Delius, H.; Kisseljov, F.;
Jenkins, N. A.; Gilbert, D. J.; Copeland, N. G.; Royer, H.-D.: Tissue
restricted expression and chromosomal localization of the YB-1 gene
encoding a 42kD nuclear CCAAT binding protein. Nucleic Acids Res. 20:
797-803, 1992.
*FIELD* CN
Paul J. Converse - updated: 4/12/2012
Patricia A. Hartz - updated: 9/1/2005
Patricia A. Hartz - updated: 8/9/2004
Patti M. Sherman - updated: 1/25/1999
*FIELD* CD
Victor A. McKusick: 10/12/1988
*FIELD* ED
alopez: 09/24/2012
mgross: 5/4/2012
terry: 4/12/2012
mgross: 9/7/2005
terry: 9/1/2005
mgross: 8/10/2004
terry: 8/9/2004
psherman: 4/3/2000
psherman: 1/25/1999
mark: 10/3/1996
terry: 9/17/1996
supermim: 3/16/1992
supermim: 3/20/1990
ddp: 10/27/1989
root: 10/17/1988
root: 10/12/1988
*RECORD*
*FIELD* NO
154030
*FIELD* TI
*154030 NUCLEASE-SENSITIVE ELEMENT-BINDING PROTEIN 1; NSEP1
;;MAJOR HISTOCOMPATIBILITY COMPLEX, CLASS II, Y BOX-BINDING PROTEIN
read more1; YB1;;
YBX1;;
DNA-BINDING PROTEIN B; DBPB
*FIELD* TX
CLONING
The expression of HLA class II genes is regulated by a series of
cis-acting elements and transacting factors. Several cis-acting elements
have been identified and have been termed the Z box, X box, Y box,
octamer, and TATA box. The Y box contains an inverted CCAAT box. Didier
et al. (1988) isolated a cDNA encoding a Y box-binding protein
designated YB1, or NSEP1. YB1 binding has an absolute requirement for
the CCAAT box and relative specificity for the Y box. It has a molecular
mass of 35,414 and contains 18% basic residues and putative nuclear
localization signals. Didier et al. (1988) found an inverse correlation
of YB1 and HLA-DR(beta) mRNA levels, suggesting that YB1 is a negative
regulatory factor.
By screening a human placenta cDNA expression library with DNA fragments
containing either the human epidermal growth factor receptor (EGFR;
131550) enhancer or the human c-erbB2 (164870) promoter, Sakura et al.
(1988) isolated cDNAs encoding DBPA (603437) and DBPB (NSEP1). The
deduced DBPA and DBPB proteins share a central region in which 100 of
109 amino acids are identical between the 2 proteins. Northern blot
analysis of HeLa cell RNA detected a 2.3-kb DBPB transcript.
Spitkovsky et al. (1992) cloned cDNAs encoding YB1 by screening a HeLa
cell cDNA expression library with an oligonucleotide containing a YB1
recognition site from the human papillomavirus type 18 enhancer. They
stated that the sequences of their cDNAs are identical to the sequence
of DBPB (Sakura et al., 1988) and nearly identical to the sequence of
the YB1 cDNA isolated by Didier et al. (1988). Northern blot analysis of
RNAs from a 24-week-old human fetus showed differential expression of
the YB1 gene. Immunoblot analysis of HeLa cell and fibroblast extracts
using antibodies against a YB1 synthetic peptide identified a 42-kD
nuclear protein.
Using an oligonucleotide containing the NSE of the MYC gene (190080)
gene as probe, Kolluri and Kinniburgh (1991) cloned NSEP1 from a HeLa
cell cDNA expression library. The deduced 322-amino acid protein
contains 4 putative DNA-binding domains, 3 of which are rich in basic
amino acids. Two of these basic regions, basic-1 and basic-2, form the
double-strand DNA-binding domain of the protein. NSEP1 also has a
pro/ser/thr-rich domain and an asp/glu/gln-rich domain, both of which
are reminiscent of activation domains. It also contains an octapeptide
single-strand DNA-binding motif that shares weak homology with the
ribonucleoprotein consensus sequence of RNA-binding proteins.
Kudo et al. (1995) isolated human cDNAs encoding DBPA and DBPB by
screening for proteins that bind to the human leukosialin (182160)
promoter. Northern blot analysis of human tissues detected the highest
DBPB expression levels in skeletal muscle and heart. The authors
isolated several DBPB processed pseudogenes and determined that they map
to many different chromosomes.
Coles et al. (1996) isolated human DBPA and DBPB cDNAs by screening for
proteins that are able to bind to the repressor element in the human
GMCSF (138960) promoter. The deduced 324-amino acid DBPB protein
contains a central cold-shock domain (CSD), which is a highly conserved,
approximately 100-amino acid domain with similarity to bacterial
cold-shock proteins. Overexpression of DBPB led to repression of the
GMCSF promoter.
GENE FUNCTION
Fukada and Tonks (2003) found that overexpression of Yb1 in Rat1 cells
resulted in increased Ptp1b (176885) expression. Depletion of Yb1
decreased Ptp1b expression, increased sensitivity to insulin, and
enhanced signaling through the cytokine receptor gp130 (IL6ST; 600694),
which was suppressed by reexpression of Ptp1b. Fukada and Tonks (2003)
also found a correlation between expression of PTP1B and YB1 in several
human cancer cell lines and in an animal model of type II diabetes (see
125853). They concluded that YB1 is an important regulator of PTP1B
expression.
Bhullar and Sollars (2011) found that Ybx1 was highly expressed in mouse
erythroid myeloid lymphoid clone-1 (EML), a hematopoietic precursor cell
line, but that it was downregulated in myeloid progenitors and in
Gmcsf-treated EML cells during myeloid differentiation.
Lineage-negative/Il7R (146661)-negative/Kit
(164920)-positive/Sca1-positive cells and
lineage-negative/Il7r-negative/Kit-positive/Sca1-negative cells
expressed high Ybx1 levels compared with differentiated cells, such as
granulocytes, in mouse bone marrow. Ybx1 was expressed at high levels in
myeloid leukemic cells at different developmental stages. Knockdown of
YBX1 in a human leukemic cell line inhibited proliferation ability,
induced apoptosis, and induced megakaryocytic differentiation in
response to arsenic trioxide treatment. Bhullar and Sollars (2011)
concluded that YBX1 is downregulated during myeloid differentiation and
that aberrant YBX1 expression in leukemic cells may contribute to
leukemia development by blocking differentiation.
GENE STRUCTURE
Makino et al. (1996) determined the nucleotide sequence of the first
exon and of 2,000 upstream nucleotides of the YB1 gene. The first exon
is unusually large and contains 166-bp coding sequence and a 331-bp
untranslated region. The GC content around the first exon is
approximately 70% and a CpG-free region was located in the untranslated
sequence. The segment preceding the major transcription initiation site
does not contain a TATA box, CCAAT box, or binding sequence for known
transcription factors. A transient expression assay using the
chloramphenicol acetyltransferase (CAT) gene showed that the sequence
from +24 to +281 was critical for CAT expression. PCR analysis on other
genomic phage DNAs showed that several clones were derived from
pseudogenes.
MAPPING
Kudo et al. (1995) mapped the human NSEP1 gene to 1p34-p33 using in situ
hybridization. By fluorescence in situ hybridization, Makino et al.
(1996) mapped the NSEP1 gene to 1p34.
*FIELD* RF
1. Bhullar, J.; Sollars, V. E.: YBX1 expression and function in early
hematopoiesis and leukemic cells. Immunogenetics 63: 337-350, 2011.
2. Coles, L. S.; Diamond, P.; Occhiodoro, F.; Vadas, M. A.; Shannon,
M. F.: Cold shock domain proteins repress transcription from the
GM-CSF promoter. Nucleic Acids Res. 24: 2311-2317, 1996.
3. Didier, D. K.; Schiffenbauer, J.; Woulfe, S. L.; Zacheis, M.; Schwartz,
B. D.: Characterization of the cDNA encoding a protein binding to
the major histocompatibility complex class II Y box. Proc. Nat. Acad.
Sci. 85: 7322-7326, 1988.
4. Fukada, T.; Tonks, N. K.: Identification of YB-1 as a regulator
of PTP1B expression: implications for regulation of insulin and cytokine
signaling. EMBO J. 22: 479-493, 2003.
5. Kolluri, R.; Kinniburgh, A. J.: Full length cDNA sequence encoding
a nuclease-sensitive element DNA binding protein. Nucleic Acids Res. 19:
4771 only, 1991.
6. Kudo, S.; Mattei, M.-G.; Fukuda, M.: Characterization of the gene
for dbpA, a family member of the nucleic-acid-binding proteins containing
a cold-shock domain. Europ. J. Biochem. 231: 72-82, 1995.
7. Makino, Y.; Ohga, T.; Toh, S.; Koike, K.; Okumura, K.; Wada, M.;
Kuwano, M.; Kohno, K.: Structural and functional analysis of the
human Y-box binding protein (YB-1) gene promoter. Nucleic Acid Res. 24:
1873-1878, 1996.
8. Sakura, H.; Maekawa, T.; Imamoto, F.; Yasuda, K.; Ishii, S.: Two
human genes isolated by a novel method encode DNA-binding proteins
containing a common region of homology. Gene 73: 499-507, 1988.
9. Spitkovsky, D. D.; Royer-Pokora, B.; Delius, H.; Kisseljov, F.;
Jenkins, N. A.; Gilbert, D. J.; Copeland, N. G.; Royer, H.-D.: Tissue
restricted expression and chromosomal localization of the YB-1 gene
encoding a 42kD nuclear CCAAT binding protein. Nucleic Acids Res. 20:
797-803, 1992.
*FIELD* CN
Paul J. Converse - updated: 4/12/2012
Patricia A. Hartz - updated: 9/1/2005
Patricia A. Hartz - updated: 8/9/2004
Patti M. Sherman - updated: 1/25/1999
*FIELD* CD
Victor A. McKusick: 10/12/1988
*FIELD* ED
alopez: 09/24/2012
mgross: 5/4/2012
terry: 4/12/2012
mgross: 9/7/2005
terry: 9/1/2005
mgross: 8/10/2004
terry: 8/9/2004
psherman: 4/3/2000
psherman: 1/25/1999
mark: 10/3/1996
terry: 9/17/1996
supermim: 3/16/1992
supermim: 3/20/1990
ddp: 10/27/1989
root: 10/17/1988
root: 10/12/1988