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Protein

Y-box-binding protein 3

Gene

YBX3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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).By similarity

GO - Molecular functioni

GO - Biological processi

  • 3'-UTR-mediated mRNA stabilization Source: BHF-UCL
  • cellular hyperosmotic response Source: BHF-UCL
  • cellular response to tumor necrosis factor Source: BHF-UCL
  • fertilization Source: Ensembl
  • in utero embryonic development Source: Ensembl
  • male gonad development Source: Ensembl
  • negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress Source: BHF-UCL
  • negative regulation of necroptotic process Source: BHF-UCL
  • negative regulation of skeletal muscle tissue development Source: Ensembl
  • negative regulation of transcription by RNA polymerase II Source: ProtInc
  • positive regulation of cytoplasmic translation Source: BHF-UCL
  • positive regulation of organ growth Source: Ensembl
  • response to cold Source: ProtInc
  • spermatogenesis Source: Ensembl
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionDNA-binding, Repressor
Biological processTranscription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:YBX3
Synonyms:CSDA, DBPA
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

EuPathDBiHostDB:ENSG00000060138.12
HGNCiHGNC:2428 YBX3
MIMi603437 gene
neXtProtiNX_P16989

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi8531
OpenTargetsiENSG00000060138
PharmGKBiPA26929

Polymorphism and mutation databases

BioMutaiYBX3
DMDMi97536050

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00001002142 – 372Y-box-binding protein 3Add BLAST371

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1
Modified residuei2PhosphoserineCombined sources1
Modified residuei34PhosphoserineCombined sources1
Modified residuei134PhosphoserineCombined sources1
Modified residuei201PhosphoserineCombined sources1
Modified residuei203PhosphoserineCombined sources1
Modified residuei204PhosphoserineCombined sources1
Modified residuei251Omega-N-methylarginineCombined sources1
Modified residuei324PhosphoserineCombined sources1
Modified residuei326Omega-N-methylarginineCombined sources1
Modified residuei346PhosphoserineBy similarity1
Modified residuei369PhosphoserineBy similarity1
Modified residuei370PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Methylation, Phosphoprotein

Proteomic databases

EPDiP16989
MaxQBiP16989
PaxDbiP16989
PeptideAtlasiP16989
PRIDEiP16989
ProteomicsDBi53404
53405 [P16989-2]
53406 [P16989-3]

PTM databases

iPTMnetiP16989
PhosphoSitePlusiP16989

Miscellaneous databases

PMAP-CutDBiP16989

Expressioni

Tissue specificityi

Highly expressed in skeletal muscle and heart.

Gene expression databases

BgeeiENSG00000060138
CleanExiHS_CSDA
ExpressionAtlasiP16989 baseline and differential
GenevisibleiP16989 HS

Organism-specific databases

HPAiHPA034838

Interactioni

Subunit structurei

Found in a mRNP complex with YBX2 (By similarity). Interacts with RRP1B (PubMed:19710015).By similarity1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
PPP1CAP621363EBI-358193,EBI-357253

GO - Molecular functioni

Protein-protein interaction databases

BioGridi114101, 112 interactors
CORUMiP16989
DIPiDIP-42489N
IntActiP16989, 49 interactors
MINTiP16989
STRINGi9606.ENSP00000228251

Structurei

3D structure databases

ProteinModelPortaliP16989
SMRiP16989
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini93 – 157CSDAdd BLAST65

Phylogenomic databases

eggNOGiKOG3070 Eukaryota
COG1278 LUCA
GeneTreeiENSGT00880000137907
HOGENOMiHOG000116439
HOVERGENiHBG008757
InParanoidiP16989
KOiK06099
OMAiQQVHRNP
OrthoDBiEOG091G0W9A
PhylomeDBiP16989
TreeFamiTF317306

Family and domain databases

CDDicd04458 CSP_CDS, 1 hit
InterProiView protein in InterPro
IPR019844 Cold-shock_CS
IPR011129 CSD
IPR002059 CSP_DNA-bd
IPR012340 NA-bd_OB-fold
PfamiView protein in Pfam
PF00313 CSD, 1 hit
PRINTSiPR00050 COLDSHOCK
SMARTiView protein in SMART
SM00357 CSP, 1 hit
SUPFAMiSSF50249 SSF50249, 1 hit
PROSITEiView protein in PROSITE
PS00352 CSD_1, 1 hit
PS51857 CSD_2, 1 hit

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist.
Isoform 1 (identifier: P16989-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MSEAGEATTT TTTTLPQAPT EAAAAAPQDP APKSPVGSGA PQAAAPAPAA
60 70 80 90 100
HVAGNPGGDA APAATGTAAA ASLATAAGSE DAEKKVLATK VLGTVKWFNV
110 120 130 140 150
RNGYGFINRN DTKEDVFVHQ TAIKKNNPRK YLRSVGDGET VEFDVVEGEK
160 170 180 190 200
GAEAANVTGP DGVPVEGSRY AADRRRYRRG YYGRRRGPPR NYAGEEEEEG
210 220 230 240 250
SGSSEGFDPP ATDRQFSGAR NQLRRPQYRP QYRQRRFPPY HVGQTFDRRS
260 270 280 290 300
RVLPHPNRIQ AGEIGEMKDG VPEGAQLQGP VHRNPTYRPR YRSRGPPRPR
310 320 330 340 350
PAPAVGEAED KENQQATSGP NQPSVRRGYR RPYNYRRRPR PPNAPSQDGK
360 370
EAKAGEAPTE NPAPPTQQSS AE
Length:372
Mass (Da):40,090
Last modified:May 16, 2006 - v4
Checksum:iAA8517AC3B7D35CC
GO
Isoform 2 (identifier: P16989-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     192-260: Missing.

Show »
Length:303
Mass (Da):31,947
Checksum:i29E708D6FCB442CD
GO
Isoform 3 (identifier: P16989-3) [UniParc]FASTAAdd to basket

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

Show »
Length:342
Mass (Da):37,021
Checksum:i255258C4B4E80A4F
GO

Sequence cautioni

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

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_01311475T → A3 PublicationsCorresponds to variant dbSNP:rs1126501Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_001135192 – 260Missing in isoform 2. 1 PublicationAdd BLAST69
Alternative sequenceiVSP_001136340 – 372RPPNA…QSSAE → PSS in isoform 3. 1 PublicationAdd BLAST33

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M24069 mRNA Translation: AAA35749.1 Different initiation.
L29071
, 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
CCDSiCCDS44831.1 [P16989-2]
CCDS8630.1 [P16989-1]
PIRiI53354
S69501
RefSeqiNP_001138898.1, NM_001145426.1 [P16989-2]
NP_003642.3, NM_003651.4 [P16989-1]
UniGeneiHs.221889

Genome annotation databases

EnsembliENST00000228251; ENSP00000228251; ENSG00000060138 [P16989-1]
ENST00000279550; ENSP00000279550; ENSG00000060138 [P16989-2]
GeneIDi8531
KEGGihsa:8531
UCSCiuc001qyt.4 human [P16989-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiYBOX3_HUMAN
AccessioniPrimary (citable) accession number: P16989
Secondary accession number(s): B2RBW6
, Q14121, Q969N6, Q96B76
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: May 16, 2006
Last modified: June 20, 2018
This is version 194 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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