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P16989 (YBOX3_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 153. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Y-box-binding protein 3
Alternative name(s):
Cold shock domain-containing protein A
DNA-binding protein A
Single-strand DNA-binding protein NF-GMB
Gene names
Name:YBX3
Synonyms:CSDA, DBPA
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length372 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 the GM-CSF promoter. Seems to act as a repressor. Binds also to full length mRNA and to short RNA sequences containing the consensus site 5'-UCCAUCA-3'. May have a role in translation repression By similarity.

Subunit structure

Found in a mRNP complex with YBX2 By similarity.

Subcellular location

Cytoplasm. Nucleus.

Tissue specificity

Highly expressed in skeletal muscle and heart.

Sequence similarities

Contains 1 CSD (cold-shock) domain.

Sequence caution

The sequence AAA35749.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentCytoplasm
Nucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   LigandDNA-binding
   Molecular functionRepressor
   PTMAcetylation
Phosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_process3'-UTR-mediated mRNA stabilization

Inferred by curator PubMed 22711822. Source: BHF-UCL

cellular hyperosmotic response

Inferred from mutant phenotype PubMed 22711822. Source: BHF-UCL

cellular response to tumor necrosis factor

Inferred from mutant phenotype PubMed 22711822. Source: BHF-UCL

fertilization

Inferred from electronic annotation. Source: Ensembl

in utero embryonic development

Inferred from electronic annotation. Source: Ensembl

male gonad development

Inferred from electronic annotation. Source: Ensembl

negative regulation of apoptotic process

Inferred from electronic annotation. Source: Ensembl

negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress

Inferred from mutant phenotype PubMed 22711822. Source: BHF-UCL

negative regulation of necroptotic process

Inferred from mutant phenotype PubMed 22711822. Source: BHF-UCL

negative regulation of skeletal muscle tissue development

Inferred from electronic annotation. Source: Ensembl

negative regulation of transcription from RNA polymerase II promoter

Traceable author statement Ref.3. Source: ProtInc

positive regulation of cytoplasmic translation

Inferred from sequence or structural similarity PubMed 22711822. Source: BHF-UCL

positive regulation of organ growth

Inferred from electronic annotation. Source: Ensembl

response to cold

Traceable author statement Ref.3. Source: ProtInc

spermatogenesis

Inferred from electronic annotation. Source: Ensembl

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcytoplasm

Inferred from direct assay. Source: HPA

nucleus

Inferred from sequence or structural similarity PubMed 22711822. Source: BHF-UCL

perinuclear region of cytoplasm

Inferred from sequence or structural similarity PubMed 22711822. Source: BHF-UCL

polysome

Inferred from electronic annotation. Source: Ensembl

tight junction

Inferred from sequence or structural similarity PubMed 22711822. Source: BHF-UCL

   Molecular_functionRho GTPase binding

Inferred from sequence or structural similarity. Source: BHF-UCL

double-stranded DNA binding

Traceable author statement Ref.1. Source: ProtInc

mRNA 3'-UTR binding

Inferred from sequence or structural similarity PubMed 22711822. Source: BHF-UCL

poly(A) RNA binding

Inferred from direct assay PubMed 22658674PubMed 22681889. Source: UniProtKB

sequence-specific DNA binding transcription factor activity

Non-traceable author statement Ref.3. Source: ProtInc

single-stranded DNA binding

Inferred from electronic annotation. Source: Ensembl

transcription corepressor activity

Traceable author statement Ref.3. Source: ProtInc

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: P16989-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: P16989-2)

The sequence of this isoform differs from the canonical sequence as follows:
     192-260: Missing.
Isoform 3 (identifier: P16989-3)

The sequence of this isoform differs from the canonical sequence as follows:
     340-372: RPPNAPSQDGKEAKAGEAPTENPAPPTQQSSAE → PSS

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.9
Chain2 – 372371Y-box-binding protein 3
PRO_0000100214

Regions

Domain93 – 15765CSD

Amino acid modifications

Modified residue21N-acetylserine Ref.9 Ref.14
Modified residue1341Phosphoserine Ref.10
Modified residue2011Phosphoserine Ref.8 Ref.10
Modified residue2031Phosphoserine Ref.8 Ref.10
Modified residue2041Phosphoserine Ref.8 Ref.10 Ref.11
Modified residue3241Phosphoserine Ref.13

Natural variations

Alternative sequence192 – 26069Missing in isoform 2.
VSP_001135
Alternative sequence340 – 37233RPPNA…QSSAE → PSS in isoform 3.
VSP_001136
Natural variant751T → A. Ref.1 Ref.2 Ref.7
Corresponds to variant rs1126501 [ dbSNP | Ensembl ].
VAR_013114

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified May 16, 2006. Version 4.
Checksum: AA8517AC3B7D35CC

FASTA37240,090
        10         20         30         40         50         60 
MSEAGEATTT TTTTLPQAPT EAAAAAPQDP APKSPVGSGA PQAAAPAPAA HVAGNPGGDA 

        70         80         90        100        110        120 
APAATGTAAA ASLATAAGSE DAEKKVLATK VLGTVKWFNV RNGYGFINRN DTKEDVFVHQ 

       130        140        150        160        170        180 
TAIKKNNPRK YLRSVGDGET VEFDVVEGEK GAEAANVTGP DGVPVEGSRY AADRRRYRRG 

       190        200        210        220        230        240 
YYGRRRGPPR NYAGEEEEEG SGSSEGFDPP ATDRQFSGAR NQLRRPQYRP QYRQRRFPPY 

       250        260        270        280        290        300 
HVGQTFDRRS RVLPHPNRIQ AGEIGEMKDG VPEGAQLQGP VHRNPTYRPR YRSRGPPRPR 

       310        320        330        340        350        360 
PAPAVGEAED KENQQATSGP NQPSVRRGYR RPYNYRRRPR PPNAPSQDGK EAKAGEAPTE 

       370 
NPAPPTQQSS AE 

« Hide

Isoform 2 [UniParc].

Checksum: 29E708D6FCB442CD
Show »

FASTA30331,947
Isoform 3 [UniParc].

Checksum: 255258C4B4E80A4F
Show »

FASTA34237,021

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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), VARIANT ALA-75.
[2]"Characterization of the gene for dbpA, a family member of the nucleic-acid-binding proteins containing a cold-shock domain."
Kudo S., Mattei M.-G., Fukuda M.
Eur. J. Biochem. 231:72-82(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], ALTERNATIVE SPLICING, VARIANT ALA-75.
Tissue: Placenta.
[3]"Cold shock domain proteins repress transcription from the GM-CSF promoter."
Coles L.S., Diamond P., Occhiodoro F., Vadas M.A., Shannon M.F.
Nucleic Acids Res. 24:2311-2317(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[4]Moschonas N.K.
Submitted (MAR-1993) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
Tissue: Blood.
[5]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[7]"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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2), VARIANT ALA-75.
Tissue: Kidney, Lung, Lymph and Muscle.
[8]"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] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-201; SER-203 AND SER-204, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[9]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
[10]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-134; SER-201; SER-203 AND SER-204, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[11]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
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.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-204, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[12]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-324, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"Comparative large-scale characterisation of plant vs. mammal proteins reveals similar and idiosyncratic N-alpha acetylation features."
Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T., Giglione C.
Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M24069 mRNA. Translation: AAA35749.1. Different initiation.
L29071 expand/collapse EMBL AC list , L29064, L29065, L29066, L29067, L29068, L29069, L29070 Genomic DNA. Translation: AAA79243.1.
X95325 mRNA. Translation: CAA64631.1.
X72712 mRNA. Translation: CAA51261.1.
AK314846 mRNA. Translation: BAG37363.1.
CH471094 Genomic DNA. Translation: EAW96201.1.
CH471094 Genomic DNA. Translation: EAW96203.1.
BC008801 mRNA. Translation: AAH08801.1.
BC015564 mRNA. Translation: AAH15564.1.
BC015913 mRNA. Translation: AAH15913.1.
BC021926 mRNA. Translation: AAH21926.1.
CCDSCCDS44831.1. [P16989-2]
CCDS8630.1. [P16989-1]
PIRI53354.
S69501.
RefSeqNP_001138898.1. NM_001145426.1. [P16989-2]
NP_003642.3. NM_003651.4. [P16989-1]
UniGeneHs.221889.

3D structure databases

ProteinModelPortalP16989.
SMRP16989. Positions 84-160.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114101. 64 interactions.
DIPDIP-42489N.
IntActP16989. 27 interactions.
MINTMINT-1152000.
STRING9606.ENSP00000228251.

PTM databases

PhosphoSiteP16989.

Polymorphism databases

DMDM97536050.

Proteomic databases

MaxQBP16989.
PaxDbP16989.
PRIDEP16989.

Protocols and materials databases

DNASU8531.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000228251; ENSP00000228251; ENSG00000060138. [P16989-1]
ENST00000279550; ENSP00000279550; ENSG00000060138. [P16989-2]
GeneID8531.
KEGGhsa:8531.
UCSCuc001qyt.3. human. [P16989-1]
uc001qyu.3. human. [P16989-2]

Organism-specific databases

CTD8531.
GeneCardsGC12M010852.
HGNCHGNC:2428. YBX3.
HPAHPA034838.
MIM603437. gene.
neXtProtNX_P16989.
PharmGKBPA26929.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1278.
HOGENOMHOG000116439.
HOVERGENHBG008757.
InParanoidP16989.
KOK06099.
OMALSFNRND.
OrthoDBEOG7TBC44.
PhylomeDBP16989.
TreeFamTF317306.

Gene expression databases

BgeeP16989.
CleanExHS_CSDA.
GenevestigatorP16989.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
InterProIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamPF00313. CSD. 1 hit.
[Graphical view]
PRINTSPR00050. COLDSHOCK.
SMARTSM00357. CSP. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 1 hit.
PROSITEPS00352. COLD_SHOCK. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSCSDA. human.
GeneWikiCSDA_(gene).
GenomeRNAi8531.
NextBio31948.
PMAP-CutDBP16989.
PROP16989.
SOURCESearch...

Entry information

Entry nameYBOX3_HUMAN
AccessionPrimary (citable) accession number: P16989
Secondary accession number(s): B2RBW6 expand/collapse secondary AC list , Q14121, Q969N6, Q96B76
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: May 16, 2006
Last modified: July 9, 2014
This is version 153 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

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

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 12

Human chromosome 12: entries, gene names and cross-references to MIM