Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Nuclease-sensitive element-binding protein 1

Gene

YBX1

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

Functioni

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.By similarity8 Publications
The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionActivator, DNA-binding, Mitogen, Repressor, RNA-binding
Biological processmRNA processing, mRNA splicing, Transcription, Transcription regulation

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-9017802 Noncanonical activation of NOTCH3
SignaLinkiP67809
SIGNORiP67809

Names & Taxonomyi

Protein namesi
Recommended name:
Nuclease-sensitive element-binding protein 1
Alternative name(s):
CCAAT-binding transcription factor I subunit A
Short name:
CBF-A
DNA-binding protein B
Short name:
DBPB
Enhancer factor I subunit A
Short name:
EFI-A
Y-box transcription factor
Y-box-binding protein 1
Short name:
YB-1
Gene namesi
Name:YBX1
Synonyms:NSEP1, YB1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

EuPathDBiHostDB:ENSG00000065978.17
HGNCiHGNC:8014 YBX1
MIMi154030 gene
neXtProtiNX_P67809

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, Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi102S → A: Loss of phosphorylation by PKB/AKT1. Inhibits translocation to the nucleus and tumor cell growth. 1 Publication1
Mutagenesisi301K → A: Abrogates unconventional secretion. 1 Publication1
Mutagenesisi304K → A: Abrogates unconventional secretion. 1 Publication1

Organism-specific databases

DisGeNETi4904
OpenTargetsiENSG00000065978
PharmGKBiPA31791

Polymorphism and mutation databases

BioMutaiYBX1
DMDMi54040031

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources1 Publication
ChainiPRO_00001002192 – 324Nuclease-sensitive element-binding protein 1Add BLAST323

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1 Publication1
Cross-linki26Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei102Phosphoserine; by PKB/AKT1Combined sources1 Publication1
Cross-linki137Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Modified residuei162PhosphotyrosineCombined sources1
Modified residuei165PhosphoserineCombined sources1 Publication1
Modified residuei167PhosphoserineCombined sources1
Modified residuei174PhosphoserineCombined sources1
Modified residuei176PhosphoserineCombined sources1
Modified residuei301N6-acetyllysine1 Publication1
Modified residuei304N6-acetyllysine1 Publication1
Modified residuei314PhosphoserineCombined sources1

Post-translational modificationi

Ubiquitinated by RBBP6; leading to a decrease of YBX1 transcactivational ability.1 Publication
In the absence of phosphorylation the protein is retained in the cytoplasm.2 Publications
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).By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei219 – 220Cleavage; by 20S proteasomal protease2

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiP67809
MaxQBiP67809
PaxDbiP67809
PeptideAtlasiP67809
PRIDEiP67809
ProteomicsDBi57522
TopDownProteomicsiP67809

PTM databases

iPTMnetiP67809
PhosphoSitePlusiP67809
SwissPalmiP67809

Miscellaneous databases

PMAP-CutDBiP67809

Expressioni

Gene expression databases

BgeeiENSG00000065978 Expressed in 94 organ(s), highest expression level in testis
CleanExiHS_YBX1
ExpressionAtlasiP67809 baseline and differential
GenevisibleiP67809 HS

Organism-specific databases

HPAiCAB005875
HPA040304
HPA057159

Interactioni

Subunit structurei

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).By similarity15 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi110959, 292 interactors
ComplexPortaliCPX-1080 CRD-mediated mRNA stability complex
CORUMiP67809
DIPiDIP-29405N
IntActiP67809, 316 interactors
MINTiP67809
STRINGi9606.ENSP00000361626

Structurei

Secondary structure

1324
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP67809
SMRiP67809
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP67809

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini61 – 125CSDAdd BLAST65

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni15 – 71Interaction with ss-DNAAdd BLAST57

Phylogenomic databases

eggNOGiKOG3070 Eukaryota
COG1278 LUCA
GeneTreeiENSGT00930000150863
HOGENOMiHOG000116439
HOVERGENiHBG008757
InParanoidiP67809
KOiK09276
OMAiYQSDGEG
PhylomeDBiP67809
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

Sequence (1+)i

Sequence statusi: Complete.

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

This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All

P67809-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSSEAETQQP PAAPPAAPAL SAADTKPGTT GSGAGSGGPG GLTSAAPAGG
60 70 80 90 100
DKKVIATKVL GTVKWFNVRN GYGFINRNDT KEDVFVHQTA IKKNNPRKYL
110 120 130 140 150
RSVGDGETVE FDVVEGEKGA EAANVTGPGG VPVQGSKYAA DRNHYRRYPR
160 170 180 190 200
RRGPPRNYQQ NYQNSESGEK NEGSESAPEG QAQQRRPYRR RRFPPYYMRR
210 220 230 240 250
PYGRRPQYSN PPVQGEVMEG ADNQGAGEQG RPVRQNMYRG YRPRFRRGPP
260 270 280 290 300
RQRQPREDGN EEDKENQGDE TQGQQPPQRR YRRNFNYRRR RPENPKPQDG
310 320
KETKAADPPA ENSSAPEAEQ GGAE
Length:324
Mass (Da):35,924
Last modified:January 23, 2007 - v3
Checksum:iDF0114BF974AEDB8
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0Y449H0Y449_HUMAN
Nuclease-sensitive element-binding ...
YBX1
374Annotation score:
C9J5V9C9J5V9_HUMAN
Nuclease-sensitive element-binding ...
YBX1
216Annotation score:

Sequence cautioni

The sequence AAA35750 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence AAA59949 differs from that shown. Reason: Frameshift at several positions.Curated
The sequence AAA61308 differs from that shown. Reason: Frameshift at position 314.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti120A → E in AAA61308 (PubMed:3174636).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M24070 mRNA Translation: AAA35750.1 Different initiation.
J03827 mRNA Translation: AAA61308.1 Frameshift.
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
CCDSiCCDS470.1
PIRiI39382
S34426
RefSeqiNP_004550.2, NM_004559.4
UniGeneiHs.473583

Genome annotation databases

EnsembliENST00000321358; ENSP00000361626; ENSG00000065978
GeneIDi4904
KEGGihsa:4904
UCSCiuc001chs.4 human

Similar proteinsi

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M24070 mRNA Translation: AAA35750.1 Different initiation.
J03827 mRNA Translation: AAA61308.1 Frameshift.
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
CCDSiCCDS470.1
PIRiI39382
S34426
RefSeqiNP_004550.2, NM_004559.4
UniGeneiHs.473583

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1H95NMR-A52-129[»]
ProteinModelPortaliP67809
SMRiP67809
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi110959, 292 interactors
ComplexPortaliCPX-1080 CRD-mediated mRNA stability complex
CORUMiP67809
DIPiDIP-29405N
IntActiP67809, 316 interactors
MINTiP67809
STRINGi9606.ENSP00000361626

PTM databases

iPTMnetiP67809
PhosphoSitePlusiP67809
SwissPalmiP67809

Polymorphism and mutation databases

BioMutaiYBX1
DMDMi54040031

Proteomic databases

EPDiP67809
MaxQBiP67809
PaxDbiP67809
PeptideAtlasiP67809
PRIDEiP67809
ProteomicsDBi57522
TopDownProteomicsiP67809

Protocols and materials databases

DNASUi4904
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000321358; ENSP00000361626; ENSG00000065978
GeneIDi4904
KEGGihsa:4904
UCSCiuc001chs.4 human

Organism-specific databases

CTDi4904
DisGeNETi4904
EuPathDBiHostDB:ENSG00000065978.17
GeneCardsiYBX1
H-InvDBiHIX0037767
HIX0172381
HGNCiHGNC:8014 YBX1
HPAiCAB005875
HPA040304
HPA057159
MIMi154030 gene
neXtProtiNX_P67809
OpenTargetsiENSG00000065978
PharmGKBiPA31791
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3070 Eukaryota
COG1278 LUCA
GeneTreeiENSGT00930000150863
HOGENOMiHOG000116439
HOVERGENiHBG008757
InParanoidiP67809
KOiK09276
OMAiYQSDGEG
PhylomeDBiP67809
TreeFamiTF317306

Enzyme and pathway databases

ReactomeiR-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-9017802 Noncanonical activation of NOTCH3
SignaLinkiP67809
SIGNORiP67809

Miscellaneous databases

ChiTaRSiYBX1 human
EvolutionaryTraceiP67809
GeneWikiiY_box_binding_protein_1
GenomeRNAii4904
PMAP-CutDBiP67809
PROiPR:P67809
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000065978 Expressed in 94 organ(s), highest expression level in testis
CleanExiHS_YBX1
ExpressionAtlasiP67809 baseline and differential
GenevisibleiP67809 HS

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
ProtoNetiSearch...

Entry informationi

Entry nameiYBOX1_HUMAN
AccessioniPrimary (citable) accession number: P67809
Secondary accession number(s): P16990
, P16991, Q14972, Q15325, Q5FVF0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: January 23, 2007
Last modified: November 7, 2018
This is version 165 of the entry and version 3 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again