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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)

 YBOX1_HUMAN             Reviewed;         324 AA.
P67809; P16990; P16991; Q14972; Q15325; Q5FVF0;
11-OCT-2004, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
23-MAY-2018, entry version 161.
RecName: Full=Nuclease-sensitive element-binding protein 1;
AltName: Full=CCAAT-binding transcription factor I subunit A;
Short=CBF-A;
AltName: Full=DNA-binding protein B;
Short=DBPB;
AltName: Full=Enhancer factor I subunit A;
Short=EFI-A;
AltName: Full=Y-box transcription factor;
AltName: Full=Y-box-binding protein 1;
Short=YB-1;
Name=YBX1; Synonyms=NSEP1, YB1;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=2977358; DOI=10.1016/0378-1119(88)90514-8;
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).
[2]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=3174636; DOI=10.1073/pnas.85.19.7322;
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. Natl. Acad. Sci. U.S.A. 85:7322-7326(1988).
[3]
NUCLEOTIDE SEQUENCE [MRNA].
PubMed=1891370; DOI=10.1093/nar/19.17.4771;
Kolluri R., Kinniburgh A.J.;
"Full length cDNA sequence encoding a nuclease-sensitive element DNA
binding protein.";
Nucleic Acids Res. 19:4771-4771(1991).
[4]
NUCLEOTIDE SEQUENCE [MRNA].
TISSUE=Bone marrow;
PubMed=8188694;
Horwitz E.M., Maloney K.A., Ley T.J.;
"A human protein containing a 'cold shock' domain binds specifically
to H-DNA upstream from the human gamma-globin genes.";
J. Biol. Chem. 269:14130-14139(1994).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Adrenal cortex, Eye, Kidney, Muscle, Placenta, Skin, Testis,
and Uterus;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[6]
PROTEIN SEQUENCE OF 2-53; 70-93; 102-137; 157-185; 205-231; 257-279
AND 305-324, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2,
PHOSPHORYLATION AT SER-165, AND IDENTIFICATION BY MASS SPECTROMETRY.
TISSUE=Ovarian carcinoma;
Bienvenut W.V.;
Submitted (JAN-2010) to UniProtKB.
[7]
FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
PubMed=10817758;
Chen C.-Y., Gherzi R., Andersen J.S., Gaietta G., Juerchott K.,
Royer H.-D., Mann M., Karin M.;
"Nucleolin and YB-1 are required for JNK-mediated interleukin-2 mRNA
stabilization during T-cell activation.";
Genes Dev. 14:1236-1248(2000).
[8]
FUNCTION.
PubMed=11698476; DOI=10.4049/jimmunol.167.10.5970;
Capowski E.E., Esnault S., Bhattacharya S., Malter J.S.;
"Y box-binding factor promotes eosinophil survival by stabilizing
granulocyte-macrophage colony-stimulating factor mRNA.";
J. Immunol. 167:5970-5976(2001).
[9]
FUNCTION, INTERACTION WITH SFRS9, AND SUBCELLULAR LOCATION.
PubMed=12604611; DOI=10.1074/jbc.M212518200;
Raffetseder U., Frye B., Rauen T., Juerchott K., Royer H.-D.,
Jansen P.L., Mertens P.R.;
"Splicing factor SRp30c interaction with Y-box protein-1 confers
nuclear YB-1 shuttling and alternative splice site selection.";
J. Biol. Chem. 278:18241-18248(2003).
[10]
INTERACTION WITH SFRS12.
PubMed=14559993; DOI=10.1128/MCB.23.21.7437-7447.2003;
Li J., Hawkins I.C., Harvey C.D., Jennings J.L., Link A.J.,
Patton J.G.;
"Regulation of alternative splicing by SRrp86 and its interacting
proteins.";
Mol. Cell. Biol. 23:7437-7447(2003).
[11]
INTERACTION WITH ANKRD2.
PubMed=15136035; DOI=10.1016/j.jmb.2004.03.071;
Kojic S., Medeot E., Guccione E., Krmac H., Zara I., Martinelli V.,
Valle G., Faulkner G.;
"The Ankrd2 protein, a link between the sarcomere and the nucleus in
skeletal muscle.";
J. Mol. Biol. 339:313-325(2004).
[12]
FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, AND INTERACTION WITH
ALYREF/THOC4; NCL; XRCC5; WRN AND MSH2.
PubMed=14718551; DOI=10.1093/nar/gkh170;
Gaudreault I., Guay D., Lebel M.;
"YB-1 promotes strand separation in vitro of duplex DNA containing
either mispaired bases or cisplatin modifications, exhibits
endonucleolytic activities and binds several DNA repair proteins.";
Nucleic Acids Res. 32:316-327(2004).
[13]
IDENTIFICATION IN A COMPLEX WITH THE U11/U12 SPLICEOSOME, AND
IDENTIFICATION BY MASS SPECTROMETRY.
PubMed=15146077; DOI=10.1261/rna.7320604;
Will C.L., Schneider C., Hossbach M., Urlaub H., Rauhut R.,
Elbashir S., Tuschl T., Luehrmann R.;
"The human 18S U11/U12 snRNP contains a set of novel proteins not
found in the U2-dependent spliceosome.";
RNA 10:929-941(2004).
[14]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-162, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=15592455; DOI=10.1038/nbt1046;
Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H.,
Zha X.-M., Polakiewicz R.D., Comb M.J.;
"Immunoaffinity profiling of tyrosine phosphorylation in cancer
cells.";
Nat. Biotechnol. 23:94-101(2005).
[15]
PHOSPHORYLATION AT SER-102, INTERACTION WITH AKT1, SUBCELLULAR
LOCATION, AND MUTAGENESIS OF SER-102.
PubMed=15806160; DOI=10.1038/sj.onc.1208590;
Sutherland B.W., Kucab J., Wu J., Lee C., Cheang M.C.U., Yorida E.,
Turbin D., Dedhar S., Nelson C., Pollak M., Leighton Grimes H.,
Miller K., Badve S., Huntsman D., Blake-Gilks C., Chen M.,
Pallen C.J., Dunn S.E.;
"Akt phosphorylates the Y-box binding protein 1 at Ser102 located in
the cold shock domain and affects the anchorage-independent growth of
breast cancer cells.";
Oncogene 24:4281-4292(2005).
[16]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174 AND SER-176, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=17081983; DOI=10.1016/j.cell.2006.09.026;
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P.,
Mann M.;
"Global, in vivo, and site-specific phosphorylation dynamics in
signaling networks.";
Cell 127:635-648(2006).
[17]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=16964243; DOI=10.1038/nbt1240;
Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P.;
"A probability-based approach for high-throughput protein
phosphorylation analysis and site localization.";
Nat. Biotechnol. 24:1285-1292(2006).
[18]
INTERACTION WITH AGO1 AND AGO2.
PubMed=17932509; DOI=10.1038/sj.embor.7401088;
Hoeck J., Weinmann L., Ender C., Ruedel S., Kremmer E., Raabe M.,
Urlaub H., Meister G.;
"Proteomic and functional analysis of Argonaute-containing mRNA-
protein complexes in human cells.";
EMBO Rep. 8:1052-1060(2007).
[19]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Prostate cancer;
PubMed=17487921; DOI=10.1002/elps.200600782;
Giorgianni F., Zhao Y., Desiderio D.M., Beranova-Giorgianni S.;
"Toward a global characterization of the phosphoproteome in prostate
cancer cells: identification of phosphoproteins in the LNCaP cell
line.";
Electrophoresis 28:2027-2034(2007).
[20]
IDENTIFICATION IN A MRNP GRANULE COMPLEX, INTERACTION WITH IGF2BP1,
SUBCELLULAR LOCATION, AND IDENTIFICATION BY MASS SPECTROMETRY.
PubMed=17289661; DOI=10.1074/mcp.M600346-MCP200;
Joeson L., Vikesaa J., Krogh A., Nielsen L.K., Hansen T., Borup R.,
Johnsen A.H., Christiansen J., Nielsen F.C.;
"Molecular composition of IMP1 ribonucleoprotein granules.";
Mol. Cell. Proteomics 6:798-811(2007).
[21]
INTERACTION WITH RBBP6, AND UBIQUITINATION.
PubMed=18851979; DOI=10.1016/j.jmb.2008.09.060;
Chibi M., Meyer M., Skepu A., Rees D.J.G., Moolman-Smook J.C.,
Pugh D.J.;
"RBBP6 interacts with multifunctional protein YB-1 through its RING
finger domain, leading to ubiquitination and proteosomal degradation
of YB-1.";
J. Mol. Biol. 384:908-916(2008).
[22]
FUNCTION, INTERACTION WITH MBNL1, SUBCELLULAR LOCATION, AND
IDENTIFICATION BY MASS SPECTROMETRY.
PubMed=18335541; DOI=10.1002/jnr.21655;
Onishi H., Kino Y., Morita T., Futai E., Sasagawa N., Ishiura S.;
"MBNL1 associates with YB-1 in cytoplasmic stress granules.";
J. Neurosci. Res. 86:1994-2002(2008).
[23]
FUNCTION, DNA-BINDING, AND INTERACTION WITH APEX1.
PubMed=18809583; DOI=10.1128/MCB.00244-08;
Chattopadhyay R., Das S., Maiti A.K., Boldogh I., Xie J., Hazra T.K.,
Kohno K., Mitra S., Bhakat K.K.;
"Regulatory role of human AP-endonuclease (APE1/Ref-1) in YB-1-
mediated activation of the multidrug resistance gene MDR1.";
Mol. Cell. Biol. 28:7066-7080(2008).
[24]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174 AND SER-176, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=18669648; DOI=10.1073/pnas.0805139105;
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
Elledge S.J., Gygi S.P.;
"A quantitative atlas of mitotic phosphorylation.";
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
[25]
ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS
SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19413330; DOI=10.1021/ac9004309;
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,
Mohammed S.;
"Lys-N and trypsin cover complementary parts of the phosphoproteome in
a refined SCX-based approach.";
Anal. Chem. 81:4493-4501(2009).
[26]
FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF LYS-301 AND LYS-304,
AND ACETYLATION AT LYS-301 AND LYS-304.
PubMed=19483673; DOI=10.1038/embor.2009.81;
Frye B.C., Halfter S., Djudjaj S., Muehlenberg P., Weber S.,
Raffetseder U., En-Nia A., Knott H., Baron J.M., Dooley S.,
Bernhagen J., Mertens P.R.;
"Y-box protein-1 is actively secreted through a non-classical pathway
and acts as an extracellular mitogen.";
EMBO Rep. 10:783-789(2009).
[27]
RNA-BINDING.
PubMed=19561594; DOI=10.1038/nbt.1550;
Ray D., Kazan H., Chan E.T., Pena Castillo L., Chaudhry S.,
Talukder S., Blencowe B.J., Morris Q., Hughes T.R.;
"Rapid and systematic analysis of the RNA recognition specificities of
RNA-binding proteins.";
Nat. Biotechnol. 27:667-670(2009).
[28]
FUNCTION, COMPONENT OF THE CRD-MEDIATED MRNA STABILIZATION COMPLEX,
IDENTIFICATION IN A MRNP COMPLEX, SUBCELLULAR LOCATION, AND
IDENTIFICATION BY MASS SPECTROMETRY.
PubMed=19029303; DOI=10.1261/rna.1175909;
Weidensdorfer D., Stoehr N., Baude A., Lederer M., Koehn M.,
Schierhorn A., Buchmeier S., Wahle E., Huettelmaiery S.;
"Control of c-myc mRNA stability by IGF2BP1-associated cytoplasmic
RNPs.";
RNA 15:104-115(2009).
[29]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-102; SER-165; SER-167;
SER-174 AND SER-176, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE
SCALE ANALYSIS].
TISSUE=Leukemic T-cell;
PubMed=19690332; DOI=10.1126/scisignal.2000007;
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
Rodionov V., Han D.K.;
"Quantitative phosphoproteomic analysis of T cell receptor signaling
reveals system-wide modulation of protein-protein interactions.";
Sci. Signal. 2:RA46-RA46(2009).
[30]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-165; SER-167; SER-174
AND SER-176, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=20068231; DOI=10.1126/scisignal.2000475;
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
Mann M.;
"Quantitative phosphoproteomics reveals widespread full
phosphorylation site occupancy during mitosis.";
Sci. Signal. 3:RA3-RA3(2010).
[31]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21269460; DOI=10.1186/1752-0509-5-17;
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
"Initial characterization of the human central proteome.";
BMC Syst. Biol. 5:17-17(2011).
[32]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-165; SER-167; SER-174;
SER-176 AND SER-314, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE
SCALE ANALYSIS].
PubMed=21406692; DOI=10.1126/scisignal.2001570;
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
Blagoev B.;
"System-wide temporal characterization of the proteome and
phosphoproteome of human embryonic stem cell differentiation.";
Sci. Signal. 4:RS3-RS3(2011).
[33]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-165; SER-174; SER-176
AND SER-314, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
TISSUE=Cervix carcinoma, and Erythroleukemia;
PubMed=23186163; DOI=10.1021/pr300630k;
Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
Mohammed S.;
"Toward a comprehensive characterization of a human cancer cell
phosphoproteome.";
J. Proteome Res. 12:260-271(2013).
[34]
INTERACTION WITH DERA, AND SUBCELLULAR LOCATION.
PubMed=25229427; DOI=10.1016/j.bbamcr.2014.09.007;
Salleron L., Magistrelli G., Mary C., Fischer N., Bairoch A., Lane L.;
"DERA is the human deoxyribose phosphate aldolase and is involved in
stress response.";
Biochim. Biophys. Acta 1843:2913-2925(2014).
[35]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-167; SER-174 AND
SER-176, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
TISSUE=Liver;
PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D.,
Wang L., Ye M., Zou H.;
"An enzyme assisted RP-RPLC approach for in-depth analysis of human
liver phosphoproteome.";
J. Proteomics 96:253-262(2014).
[36]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=25944712; DOI=10.1002/pmic.201400617;
Vaca Jacome A.S., Rabilloud T., Schaeffer-Reiss C., Rompais M.,
Ayoub D., Lane L., Bairoch A., Van Dorsselaer A., Carapito C.;
"N-terminome analysis of the human mitochondrial proteome.";
Proteomics 15:2519-2524(2015).
[37]
SUMOYLATION [LARGE SCALE ANALYSIS] AT LYS-26, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=28112733; DOI=10.1038/nsmb.3366;
Hendriks I.A., Lyon D., Young C., Jensen L.J., Vertegaal A.C.,
Nielsen M.L.;
"Site-specific mapping of the human SUMO proteome reveals co-
modification with phosphorylation.";
Nat. Struct. Mol. Biol. 24:325-336(2017).
[38]
STRUCTURE BY NMR OF 52-129, AND INTERACTION WITH SS-DNA.
PubMed=11851341; DOI=10.1006/jmbi.2001.5334;
Kloks C.P.A.M., Spronk C.A.E.M., Lasonder E., Hoffmann A.,
Vuister G.W., Grzesiek S., Hilbers C.W.;
"The solution structure and DNA-binding properties of the cold-shock
domain of the human Y-box protein YB-1.";
J. Mol. Biol. 316:317-326(2002).
-!- FUNCTION: Mediates pre-mRNA alternative splicing regulation. Binds
to splice sites in pre-mRNA and regulates splice site selection.
Binds and stabilizes cytoplasmic mRNA. Contributes to the
regulation of translation by modulating the interaction between
the mRNA and eukaryotic initiation factors (By similarity).
Regulates the transcription of numerous genes. Its transcriptional
activity on the multidrug resistance gene MDR1 is enhanced in
presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7'.
Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such
as MDR1 and HLA class II genes. Promotes separation of DNA strands
that contain mismatches or are modified by cisplatin. Has
endonucleolytic activity and can introduce nicks or breaks into
double-stranded DNA (in vitro). May play a role in DNA repair.
Component of the CRD-mediated complex that promotes MYC mRNA
stability. Binds preferentially to the 5'-[CU]CUGCG-3' motif in
vitro. {ECO:0000250, ECO:0000269|PubMed:10817758,
ECO:0000269|PubMed:11698476, ECO:0000269|PubMed:12604611,
ECO:0000269|PubMed:14718551, ECO:0000269|PubMed:18335541,
ECO:0000269|PubMed:18809583, ECO:0000269|PubMed:19029303,
ECO:0000269|PubMed:19483673}.
-!- FUNCTION: The secreted form acts as an extracellular mitogen and
stimulates cell migration and proliferation.
-!- SUBUNIT: Identified in a histone pre-mRNA complex, at least
composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (By
similarity). Component of the coding region determinant (CRD)-
mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and
YBX1. Identified in a IGF2BP1-dependent mRNP granule complex
containing untranslated mRNAs. Component of the U11/U12 snRNPs
that are part of the U12-type spliceosome. Interacts with IGF2BP1
and RBBP6. Component of cytoplasmic messenger ribonucleoprotein
particles (mRNPs). Interacts with AKT1, MBNL1, SFRS9,
ALYREF/THOC4, MSH2, XRCC5, WRN and NCL. Can bind to DNA as a
homomeric form, (EFI-A)n or as a heteromeric form in association
with EFI-B. Homodimer in the presence of ATP. Interacts (via C-
terminus) with APEX1 (via N-terminus); the interaction is
increased with APEX1 acetylated at 'Lys-6' and 'Lys-7'. Interacts
with AGO1 and AGO2. Interacts with ANKRD2. Interacts with DERA.
Interacts with FMR1; this interaction occurs in association with
polyribosome (By similarity). Interacts with ZBTB7B (By
similarity). {ECO:0000250, ECO:0000250|UniProtKB:P62960,
ECO:0000269|PubMed:10817758, ECO:0000269|PubMed:11851341,
ECO:0000269|PubMed:12604611, ECO:0000269|PubMed:14559993,
ECO:0000269|PubMed:14718551, ECO:0000269|PubMed:15136035,
ECO:0000269|PubMed:15146077, ECO:0000269|PubMed:15806160,
ECO:0000269|PubMed:17289661, ECO:0000269|PubMed:17932509,
ECO:0000269|PubMed:18335541, ECO:0000269|PubMed:18809583,
ECO:0000269|PubMed:18851979, ECO:0000269|PubMed:19029303,
ECO:0000269|PubMed:25229427}.
-!- INTERACTION:
Q07021:C1QBP; NbExp=6; IntAct=EBI-354065, EBI-347528;
Q08705:CTCF (xeno); NbExp=2; IntAct=EBI-354065, EBI-932806;
Q08211:DHX9; NbExp=10; IntAct=EBI-354065, EBI-352022;
Q09472:EP300; NbExp=2; IntAct=EBI-354065, EBI-447295;
Q7Z6M2:FBXO33; NbExp=5; IntAct=EBI-354065, EBI-8555452;
Q14103-4:HNRNPD; NbExp=3; IntAct=EBI-354065, EBI-432545;
P62310:LSM3; NbExp=2; IntAct=EBI-354065, EBI-348239;
Q99697:PITX2; NbExp=3; IntAct=EBI-354065, EBI-1175211;
O15355:PPM1G; NbExp=2; IntAct=EBI-354065, EBI-725702;
-!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Cytoplasmic granule
{ECO:0000269|PubMed:25229427}. Secreted. Note=Localized in
cytoplasmic mRNP granules containing untranslated mRNAs. Shuttles
between nucleus and cytoplasm. Predominantly cytoplasmic in
proliferating cells. Cytotoxic stress and DNA damage enhance
translocation to the nucleus. Localized with DDX1, MBNL1 and TIAL1
in stress granules upon stress. Secreted by mesangial and
monocytic cells after inflammatory challenges. Translocates from
the cytoplasm to the nucleus after and colocalizes with APEX1 in
nuclear speckles after genotoxic stress.
-!- PTM: Ubiquitinated by RBBP6; leading to a decrease of YBX1
transcactivational ability. {ECO:0000269|PubMed:18851979}.
-!- PTM: In the absence of phosphorylation the protein is retained in
the cytoplasm. {ECO:0000269|PubMed:15806160, ECO:0000269|Ref.6}.
-!- PTM: Cleaved by a 20S proteasomal protease in response to agents
that damage DNA. Cleavage takes place in the absence of
ubiquitination and ATP. The resulting N-terminal fragment
accumulates in the nucleus (By similarity).
{ECO:0000250|UniProtKB:Q28618}.
-!- SEQUENCE CAUTION:
Sequence=AAA35750.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
Sequence=AAA59949.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305};
Sequence=AAA61308.1; Type=Frameshift; Positions=314; Evidence={ECO:0000305};
-!- WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology
and Haematology;
URL="http://atlasgeneticsoncology.org/Genes/YBX1ID46554ch1p34.html";
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EMBL; M24070; AAA35750.1; ALT_INIT; mRNA.
EMBL; J03827; AAA61308.1; ALT_FRAME; mRNA.
EMBL; M83234; AAA59949.1; ALT_FRAME; mRNA.
EMBL; L28809; AAA20871.1; -; mRNA.
EMBL; BC002411; AAH02411.1; -; mRNA.
EMBL; BC010430; AAH10430.1; -; mRNA.
EMBL; BC015208; AAH15208.1; -; mRNA.
EMBL; BC038384; AAH38384.1; -; mRNA.
EMBL; BC065571; AAH65571.1; -; mRNA.
EMBL; BC070084; AAH70084.1; -; mRNA.
EMBL; BC071708; AAH71708.1; -; mRNA.
EMBL; BC090038; AAH90038.1; -; mRNA.
EMBL; BC098435; AAH98435.1; -; mRNA.
EMBL; BC106045; AAI06046.1; -; mRNA.
CCDS; CCDS470.1; -.
PIR; I39382; I39382.
PIR; S34426; S34426.
RefSeq; NP_004550.2; NM_004559.4.
UniGene; Hs.473583; -.
PDB; 1H95; NMR; -; A=52-129.
PDBsum; 1H95; -.
ProteinModelPortal; P67809; -.
SMR; P67809; -.
BioGrid; 110959; 218.
CORUM; P67809; -.
DIP; DIP-29405N; -.
IntAct; P67809; 316.
MINT; P67809; -.
STRING; 9606.ENSP00000361626; -.
iPTMnet; P67809; -.
PhosphoSitePlus; P67809; -.
SwissPalm; P67809; -.
BioMuta; YBX1; -.
DMDM; 54040031; -.
EPD; P67809; -.
MaxQB; P67809; -.
PaxDb; P67809; -.
PeptideAtlas; P67809; -.
PRIDE; P67809; -.
TopDownProteomics; P67809; -.
DNASU; 4904; -.
Ensembl; ENST00000321358; ENSP00000361626; ENSG00000065978.
GeneID; 4904; -.
KEGG; hsa:4904; -.
UCSC; uc001chs.4; human.
CTD; 4904; -.
DisGeNET; 4904; -.
EuPathDB; HostDB:ENSG00000065978.17; -.
GeneCards; YBX1; -.
H-InvDB; HIX0037767; -.
H-InvDB; HIX0172381; -.
HGNC; HGNC:8014; YBX1.
HPA; CAB005875; -.
HPA; HPA040304; -.
HPA; HPA057159; -.
MIM; 154030; gene.
neXtProt; NX_P67809; -.
OpenTargets; ENSG00000065978; -.
PharmGKB; PA31791; -.
eggNOG; KOG3070; Eukaryota.
eggNOG; COG1278; LUCA.
GeneTree; ENSGT00880000137907; -.
HOGENOM; HOG000116439; -.
HOVERGEN; HBG008757; -.
InParanoid; P67809; -.
KO; K09276; -.
OMA; RRYPPYY; -.
PhylomeDB; P67809; -.
TreeFam; TF317306; -.
Reactome; R-HSA-72163; mRNA Splicing - Major Pathway.
Reactome; R-HSA-72165; mRNA Splicing - Minor Pathway.
Reactome; R-HSA-9017802; Noncanonical activation of NOTCH3.
SignaLink; P67809; -.
SIGNOR; P67809; -.
ChiTaRS; YBX1; human.
EvolutionaryTrace; P67809; -.
GeneWiki; Y_box_binding_protein_1; -.
GenomeRNAi; 4904; -.
PMAP-CutDB; P67809; -.
PRO; PR:P67809; -.
Proteomes; UP000005640; Chromosome 1.
Bgee; ENSG00000065978; -.
CleanEx; HS_YBX1; -.
ExpressionAtlas; P67809; baseline and differential.
Genevisible; P67809; HS.
GO; GO:0070937; C:CRD-mediated mRNA stability complex; IDA:UniProtKB.
GO; GO:0005737; C:cytoplasm; IDA:AgBase.
GO; GO:0010494; C:cytoplasmic stress granule; IDA:UniProtKB.
GO; GO:0005829; C:cytosol; IDA:HPA.
GO; GO:0070062; C:extracellular exosome; HDA:UniProtKB.
GO; GO:0005576; C:extracellular region; TAS:Reactome.
GO; GO:0071204; C:histone pre-mRNA 3'end processing complex; ISS:UniProtKB.
GO; GO:0043231; C:intracellular membrane-bounded organelle; IDA:HPA.
GO; GO:0031965; C:nuclear membrane; IDA:HPA.
GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
GO; GO:0005634; C:nucleus; TAS:ProtInc.
GO; GO:1990904; C:ribonucleoprotein complex; IDA:UniProtKB.
GO; GO:0005689; C:U12-type spliceosomal complex; IDA:UniProtKB.
GO; GO:0003682; F:chromatin binding; IEA:Ensembl.
GO; GO:0003677; F:DNA binding; IDA:UniProtKB.
GO; GO:0003700; F:DNA binding transcription factor activity; TAS:ProtInc.
GO; GO:0003690; F:double-stranded DNA binding; TAS:ProtInc.
GO; GO:0051020; F:GTPase binding; IPI:UniProtKB.
GO; GO:0003723; F:RNA binding; IDA:UniProtKB.
GO; GO:0000978; F:RNA polymerase II proximal promoter sequence-specific DNA binding; IDA:NTNU_SB.
GO; GO:0000981; F:RNA polymerase II transcription factor activity, sequence-specific DNA binding; ISA:NTNU_SB.
GO; GO:0003697; F:single-stranded DNA binding; TAS:ProtInc.
GO; GO:0001077; F:transcriptional activator activity, RNA polymerase II proximal promoter sequence-specific DNA binding; IDA:NTNU_SB.
GO; GO:0070934; P:CRD-mediated mRNA stabilization; IMP:UniProtKB.
GO; GO:0001701; P:in utero embryonic development; IEA:Ensembl.
GO; GO:0000398; P:mRNA splicing, via spliceosome; TAS:Reactome.
GO; GO:0051154; P:negative regulation of striated muscle cell differentiation; IEA:Ensembl.
GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IEA:Ensembl.
GO; GO:0007219; P:Notch signaling pathway; TAS:Reactome.
GO; GO:0051781; P:positive regulation of cell division; IEA:UniProtKB-KW.
GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IDA:NTNU_SB.
GO; GO:1903608; P:protein localization to cytoplasmic stress granule; IMP:AgBase.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IDA:UniProtKB.
GO; GO:0006366; P:transcription by RNA polymerase II; TAS:ProtInc.
CDD; cd04458; CSP_CDS; 1.
InterPro; IPR019844; Cold-shock_CS.
InterPro; IPR011129; CSD.
InterPro; IPR002059; CSP_DNA-bd.
InterPro; IPR012340; NA-bd_OB-fold.
Pfam; PF00313; CSD; 1.
PRINTS; PR00050; COLDSHOCK.
SMART; SM00357; CSP; 1.
SUPFAM; SSF50249; SSF50249; 1.
PROSITE; PS00352; CSD_1; 1.
PROSITE; PS51857; CSD_2; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Activator; Complete proteome; Cytoplasm;
Direct protein sequencing; DNA-binding; Isopeptide bond; Mitogen;
mRNA processing; mRNA splicing; Nucleus; Phosphoprotein;
Reference proteome; Repressor; RNA-binding; Secreted; Transcription;
Transcription regulation; Ubl conjugation.
INIT_MET 1 1 Removed. {ECO:0000244|PubMed:19413330,
ECO:0000269|Ref.6}.
CHAIN 2 324 Nuclease-sensitive element-binding
protein 1.
/FTId=PRO_0000100219.
DOMAIN 61 125 CSD.
REGION 15 71 Interaction with ss-DNA.
SITE 219 220 Cleavage; by 20S proteasomal protease.
MOD_RES 2 2 N-acetylserine.
{ECO:0000244|PubMed:19413330,
ECO:0000269|Ref.6}.
MOD_RES 102 102 Phosphoserine; by PKB/AKT1.
{ECO:0000244|PubMed:19690332,
ECO:0000269|PubMed:15806160}.
MOD_RES 162 162 Phosphotyrosine.
{ECO:0000244|PubMed:15592455}.
MOD_RES 165 165 Phosphoserine.
{ECO:0000244|PubMed:19690332,
ECO:0000244|PubMed:20068231,
ECO:0000244|PubMed:21406692,
ECO:0000244|PubMed:23186163,
ECO:0000269|Ref.6}.
MOD_RES 167 167 Phosphoserine.
{ECO:0000244|PubMed:19690332,
ECO:0000244|PubMed:20068231,
ECO:0000244|PubMed:21406692,
ECO:0000244|PubMed:24275569}.
MOD_RES 174 174 Phosphoserine.
{ECO:0000244|PubMed:17081983,
ECO:0000244|PubMed:18669648,
ECO:0000244|PubMed:19690332,
ECO:0000244|PubMed:20068231,
ECO:0000244|PubMed:21406692,
ECO:0000244|PubMed:23186163,
ECO:0000244|PubMed:24275569}.
MOD_RES 176 176 Phosphoserine.
{ECO:0000244|PubMed:17081983,
ECO:0000244|PubMed:18669648,
ECO:0000244|PubMed:19690332,
ECO:0000244|PubMed:20068231,
ECO:0000244|PubMed:21406692,
ECO:0000244|PubMed:23186163,
ECO:0000244|PubMed:24275569}.
MOD_RES 301 301 N6-acetyllysine.
{ECO:0000269|PubMed:19483673}.
MOD_RES 304 304 N6-acetyllysine.
{ECO:0000269|PubMed:19483673}.
MOD_RES 314 314 Phosphoserine.
{ECO:0000244|PubMed:21406692,
ECO:0000244|PubMed:23186163}.
CROSSLNK 26 26 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in SUMO2).
{ECO:0000244|PubMed:28112733}.
CROSSLNK 137 137 Glycyl lysine isopeptide (Lys-Gly)
(interchain with G-Cter in ubiquitin).
{ECO:0000269|PubMed:18851979}.
MUTAGEN 102 102 S->A: Loss of phosphorylation by
PKB/AKT1. Inhibits translocation to the
nucleus and tumor cell growth.
{ECO:0000269|PubMed:15806160}.
MUTAGEN 301 301 K->A: Abrogates unconventional secretion.
{ECO:0000269|PubMed:19483673}.
MUTAGEN 304 304 K->A: Abrogates unconventional secretion.
{ECO:0000269|PubMed:19483673}.
CONFLICT 120 120 A -> E (in Ref. 2; AAA61308).
{ECO:0000305}.
STRAND 56 67 {ECO:0000244|PDB:1H95}.
TURN 68 71 {ECO:0000244|PDB:1H95}.
STRAND 72 77 {ECO:0000244|PDB:1H95}.
TURN 78 81 {ECO:0000244|PDB:1H95}.
STRAND 82 87 {ECO:0000244|PDB:1H95}.
HELIX 88 90 {ECO:0000244|PDB:1H95}.
STRAND 108 115 {ECO:0000244|PDB:1H95}.
STRAND 117 125 {ECO:0000244|PDB:1H95}.
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


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