Skip Header

 
Contribute Send feedback
Read comments (0) or add your own

Reviewed, UniProtKB/Swiss-Prot P67809 (YBOX1_HUMAN)

Last modified June 16, 2009. Version 64. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data | Customize display text xml rdf/xml gff fasta
Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

Names and origin

Protein namesRecommended name:
    Nuclease-sensitive element-binding protein 1
Alternative name(s):
    Y-box-binding protein 1
    Y-box transcription factor
    YB-1
    CCAAT-binding transcription factor I subunit A
      Short name=CBF-A
    Enhancer factor I subunit A
      Short name=EFI-A
    DNA-binding protein B
      Short name=DBPB
Gene names
Name: YBX1
Synonyms: NSEP1, YB1
OrganismHomo sapiens (Human)
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length324 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level.

General annotation (Comments)

Function

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. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as HLA class II genes. Regulates the transcription of numerous 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.

Subunit structure

Component of cytoplasmic messenger ribonucleoprotein particles (mRNPs). Interacts with AKT1, SFRS9, 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. Ref.6 Ref.8 Ref.9 Ref.10 Ref.11 Ref.19

Subcellular location

Cytoplasm. Nucleus. Note: Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in proliferating cells. Cytotoxic stress and DNA damage enhance translocation to the nucleus. Ref.8 Ref.10 Ref.11

Post-translational modification

In the absence of phosphorylation the protein is retained in the cytoplasm.

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.

Sequence similarities

Contains 1 CSD (cold-shock) domain.

Sequence caution

The sequence AAA59949.1 differs from that shown. Reason: Frameshift at several positions.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

CTCFQ087052EBI-354065,EBI-932806From a different organism.
HNRNPDQ14103-32EBI-354065,EBI-432539
HNRNPDQ14103-43EBI-354065,EBI-432545

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed
Chain2 – 324323Nuclease-sensitive element-binding protein 1
PRO_0000100219

Regions

Domain61 – 12565CSD
Region15 – 7157Interaction with ss-DNA

Sites

Site219 – 2202Cleavage; by 20S proteasomal protease

Amino acid modifications

Modified residue1021Phosphoserine; by PKB/AKT1 Ref.11
Modified residue1621Phosphotyrosine Ref.12
Modified residue1651Phosphoserine Ref.14 Ref.17
Modified residue1671Phosphoserine Ref.14
Modified residue1741Phosphoserine Ref.14 Ref.17 Ref.13
Modified residue1761Phosphoserine Ref.17 Ref.13
Modified residue3141Phosphoserine Ref.13 Ref.15
Cross-link137Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.16

Experimental info

Mutagenesis1021S → A: Loss of phosphorylation by PKB/AKT1. Inhibits translocation to the nucleus and tumor cell growth. Ref.11
Sequence conflict1201A → E in AAA61308. Ref.2
Sequence conflict314 – 32411SAPEAEQGGAE → RSR Ref.2

Secondary structure

............ 324
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P67809-1 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: DF0114BF974AEDB8

FASTA32435,924
        10         20         30         40         50         60 
MSSEAETQQP PAAPPAAPAL SAADTKPGTT GSGAGSGGPG GLTSAAPAGG DKKVIATKVL 

        70         80         90        100        110        120 
GTVKWFNVRN GYGFINRNDT KEDVFVHQTA IKKNNPRKYL RSVGDGETVE FDVVEGEKGA 

       130        140        150        160        170        180 
EAANVTGPGG VPVQGSKYAA DRNHYRRYPR RRGPPRNYQQ NYQNSESGEK NEGSESAPEG 

       190        200        210        220        230        240 
QAQQRRPYRR RRFPPYYMRR PYGRRPQYSN PPVQGEVMEG ADNQGAGEQG RPVRQNMYRG 

       250        260        270        280        290        300 
YRPRFRRGPP RQRQPREDGN EEDKENQGDE TQGQQPPQRR YRRNFNYRRR RPENPKPQDG 

       310        320 
KETKAADPPA ENSSAPEAEQ GGAE 

« Hide

References

« Hide 'large scale' references
[1]"Two human genes isolated by a novel method encode DNA-binding proteins containing a common region of homology."
Sakura H., Maekawa T., Imamoto F., Yasuda K., Ishii S.
Gene 73:499-507(1988) [PubMed: 2977358] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box."
Didier D.K., Schiffenbauer J., Woulfe S.L., Zacheis M., Schwartz B.D.
Proc. Natl. Acad. Sci. U.S.A. 85:7322-7326(1988) [PubMed: 3174636] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]"Full length cDNA sequence encoding a nuclease-sensitive element DNA binding protein."
Kolluri R., Kinniburgh A.J.
Nucleic Acids Res. 19:4771-4771(1991) [PubMed: 1891370] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[4]"A human protein containing a 'cold shock' domain binds specifically to H-DNA upstream from the human gamma-globin genes."
Horwitz E.M., Maloney K.A., Ley T.J.
J. Biol. Chem. 269:14130-14139(1994) [PubMed: 8188694] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Tissue: Bone marrow.
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Adrenal cortex, Eye, Kidney, Muscle, Placenta, Skin, Testis and Uterus.
[6]"Nucleolin and YB-1 are required for JNK-mediated interleukin-2 mRNA stabilization during T-cell activation."
Chen C.-Y., Gherzi R., Andersen J.S., Gaietta G., Juerchott K., Royer H.-D., Mann M., Karin M.
Genes Dev. 14:1236-1248(2000) [PubMed: 10817758] [Abstract]
Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT.
[7]"Y box-binding factor promotes eosinophil survival by stabilizing granulocyte-macrophage colony-stimulating factor mRNA."
Capowski E.E., Esnault S., Bhattacharya S., Malter J.S.
J. Immunol. 167:5970-5976(2001) [PubMed: 11698476] [Abstract]
Cited for: FUNCTION.
[8]"Splicing factor SRp30c interaction with Y-box protein-1 confers nuclear YB-1 shuttling and alternative splice site selection."
Raffetseder U., Frye B., Rauen T., Juerchott K., Royer H.-D., Jansen P.L., Mertens P.R.
J. Biol. Chem. 278:18241-18248(2003) [PubMed: 12604611] [Abstract]
Cited for: FUNCTION, INTERACTION WITH SFRS9, SUBCELLULAR LOCATION.
[9]"Regulation of alternative splicing by SRrp86 and its interacting proteins."
Li J., Hawkins I.C., Harvey C.D., Jennings J.L., Link A.J., Patton J.G.
Mol. Cell. Biol. 23:7437-7447(2003) [PubMed: 14559993] [Abstract]
Cited for: INTERACTION WITH SFRS12.
[10]"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."
Gaudreault I., Guay D., Lebel M.
Nucleic Acids Res. 32:316-327(2004) [PubMed: 14718551] [Abstract]
Cited for: FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, INTERACTION WITH THOC4; NCL; XRCC5; WRN AND MSH2.
[11]"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."
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.
Oncogene 24:4281-4292(2005) [PubMed: 15806160] [Abstract]
Cited for: PHOSPHORYLATION AT SER-102, INTERACTION WITH AKT1, SUBCELLULAR LOCATION, MUTAGENESIS OF SER-102.
[12]"Immunoaffinity profiling of tyrosine phosphorylation in cancer cells."
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.
Nat. Biotechnol. 23:94-101(2005) [PubMed: 15592455] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-162, MASS SPECTROMETRY.
[13]"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
Cell 127:635-648(2006) [PubMed: 17081983] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174; SER-176 AND SER-314, MASS SPECTROMETRY.
Tissue: Epithelium.
[14]"Toward a global characterization of the phosphoproteome in prostate cancer cells: identification of phosphoproteins in the LNCaP cell line."
Giorgianni F., Zhao Y., Desiderio D.M., Beranova-Giorgianni S.
Electrophoresis 28:2027-2034(2007) [PubMed: 17487921] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-165; SER-167 AND SER-174, MASS SPECTROMETRY.
[15]"Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry."
Molina H., Horn D.M., Tang N., Mathivanan S., Pandey A.
Proc. Natl. Acad. Sci. U.S.A. 104:2199-2204(2007) [PubMed: 17287340] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-314, MASS SPECTROMETRY.
[16]"Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry."
Meierhofer D., Wang X., Huang L., Kaiser P.
J. Proteome Res. 7:4566-4576(2008) [PubMed: 18781797] [Abstract]
Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-137, MASS SPECTROMETRY.
[17]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-165; SER-174 AND SER-176, MASS SPECTROMETRY.
[18]Colinge J., Superti-Furga G., Bennett K.L.
Submitted (OCT-2008) to UniProtKB
Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[19]"The solution structure and DNA-binding properties of the cold-shock domain of the human Y-box protein YB-1."
Kloks C.P.A.M., Spronk C.A.E.M., Lasonder E., Hoffmann A., Vuister G.W., Grzesiek S., Hilbers C.W.
J. Mol. Biol. 316:317-326(2002) [PubMed: 11851341] [Abstract]
Cited for: STRUCTURE BY NMR OF 52-129, INTERACTION WITH SS-DNA.
+Additional computationally mapped references.

Cross-references

Sequence databases

M24070 mRNA. Translation: AAA35750.1. Different initiation.
J03827 mRNA. Translation: AAA61308.1.
M83234 mRNA. Translation: AAA59949.1. Frameshift.
L28809 mRNA. Translation: AAA20871.1.
BC002411 mRNA. Translation: AAH02411.1.
BC010430 mRNA. Translation: AAH10430.1.
BC015208 mRNA. Translation: AAH15208.1.
BC038384 mRNA. Translation: AAH38384.1.
BC065571 mRNA. Translation: AAH65571.1.
BC070084 mRNA. Translation: AAH70084.1.
BC071708 mRNA. Translation: AAH71708.1.
BC090038 mRNA. Translation: AAH90038.1.
BC098435 mRNA. Translation: AAH98435.1.
BC106045 mRNA. Translation: AAI06046.1.
IPIIPI00031812.
PIRI39382.
S34426.
RefSeqNP_004550.2.
UniGeneHs.473583

3D structure databases

EntryMethodResolution (Å)ChainPositionsPDBsum
1H95NMR-A52-129[»]
ModBaseSearch...

Protein-protein interaction databases

IntActP67809. 13 interactions.

PTM databases

PhosphoSiteP67809.

Proteomic databases

PRIDEP67809.

Genome annotation databases

EnsemblENSG00000065978. Homo sapiens. [Contig view]
GeneID4904.
KEGGhsa:4904.

Organism-specific databases

GeneCardsGC01P042920.
H-InvDBHIX0000491.
HGNCHGNC:8014. YBX1.
HPACAB005875.
MIM154030. gene.
PharmGKBPA31791.
GenAtlasSearch...

Phylogenomic databases

HOGENOMP67809.
HOVERGENP67809.
OMAP67809. PAENTSA.

Enzyme and pathway databases

Pathway_Interaction_DBptp1bpathway. Signaling events mediated by PTP1B.
ReactomeREACT_1675. mRNA Processing.
REACT_6167. Influenza Infection.
REACT_71. Gene Expression.

Gene expression databases

CleanExHS_YBX1.
GermOnlineENSG00000065978. Homo sapiens.

Family and domain databases

InterProIPR019844. Cold-shock_conserved_site.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA_bd.
IPR012340. NA-bd_OB-fold.
[Graphical view]
Gene3DG3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
PfamPF00313. CSD. 1 hit.
[Graphical view]
PRINTSPR00050. COLDSHOCK.
ProDomPD000621. Cold_shock. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SMARTSM00357. CSP. 1 hit.
[Graphical view]
PROSITEPS00352. COLD_SHOCK. 1 hit.
[Graphical view]
ProtoNetSearch...

Other Resources

NextBio18871.
PMAP-CutDBP67809.
SOURCESearch...

Entry information

Entry nameYBOX1_HUMAN
AccessionPrimary (citable) accession number: P67809
Secondary accession number(s): P16990 expand/collapse secondary AC list , P16991, Q14972, Q15325, Q5FVF0
Entry history
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: January 23, 2007
Last modified: June 16, 2009
This is version 64 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation projectHPI (Human Proteome Initiative)

Relevant documents

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents