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Protein

Nuclease-sensitive element-binding protein 1

Gene

YBX1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

  • chromatin binding Source: Ensembl
  • DNA binding Source: UniProtKB
  • double-stranded DNA binding Source: ProtInc
  • GTPase binding Source: UniProtKB
  • poly(A) RNA binding Source: UniProtKB
  • RNA binding Source: UniProtKB
  • RNA polymerase II core promoter proximal region sequence-specific DNA binding Source: NTNU_SB
  • single-stranded DNA binding Source: ProtInc
  • transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding Source: NTNU_SB
  • transcription factor activity, sequence-specific DNA binding Source: ProtInc

GO - Biological processi

  • CRD-mediated mRNA stabilization Source: UniProtKB
  • in utero embryonic development Source: Ensembl
  • mRNA splicing, via spliceosome Source: Reactome
  • negative regulation of striated muscle cell differentiation Source: Ensembl
  • negative regulation of transcription from RNA polymerase II promoter Source: Ensembl
  • positive regulation of cell division Source: UniProtKB-KW
  • positive regulation of transcription from RNA polymerase II promoter Source: NTNU_SB
  • protein localization to cytoplasmic stress granule Source: AgBase
  • regulation of transcription, DNA-templated Source: UniProtKB
  • transcription from RNA polymerase II promoter Source: ProtInc
Complete GO annotation...

Keywords - Molecular functioni

Activator, Mitogen, Repressor

Keywords - Biological processi

mRNA processing, mRNA splicing, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000065978-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.
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

HGNCiHGNC:8014. YBX1.

Subcellular locationi

  • Cytoplasm
  • Nucleus
  • Cytoplasmic granule 1 Publication
  • 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.

GO - Cellular componenti

  • CRD-mediated mRNA stability complex Source: UniProtKB
  • cytoplasm Source: AgBase
  • cytoplasmic stress granule Source: UniProtKB
  • extracellular exosome Source: UniProtKB
  • histone pre-mRNA 3'end processing complex Source: UniProtKB
  • intracellular membrane-bounded organelle Source: HPA
  • intracellular ribonucleoprotein complex Source: UniProtKB
  • nuclear membrane Source: HPA
  • nucleoplasm Source: Reactome
  • nucleus Source: ProtInc
  • U12-type spliceosomal complex Source: UniProtKB
Complete GO annotation...

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
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.
TopDownProteomicsiP67809.

PTM databases

iPTMnetiP67809.
PhosphoSitePlusiP67809.
SwissPalmiP67809.

Miscellaneous databases

PMAP-CutDBP67809.

Expressioni

Gene expression databases

BgeeiENSG00000065978.
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).By similarity15 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
C1QBPQ070216EBI-354065,EBI-347528
CTCFQ087052EBI-354065,EBI-932806From a different organism.
DHX9Q0821110EBI-354065,EBI-352022
EP300Q094722EBI-354065,EBI-447295
FBXO33Q7Z6M25EBI-354065,EBI-8555452
HNRNPDQ14103-43EBI-354065,EBI-432545
LSM3P623102EBI-354065,EBI-348239
PITX2Q996973EBI-354065,EBI-1175211

GO - Molecular functioni

  • GTPase binding Source: UniProtKB

Protein-protein interaction databases

BioGridi110959. 194 interactors.
DIPiDIP-29405N.
IntActiP67809. 312 interactors.
MINTiMINT-5001202.
STRINGi9606.ENSP00000361626.

Structurei

Secondary structure

1324
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi56 – 67Combined sources12
Turni68 – 71Combined sources4
Beta strandi72 – 77Combined sources6
Turni78 – 81Combined sources4
Beta strandi82 – 87Combined sources6
Helixi88 – 90Combined sources3
Beta strandi108 – 115Combined sources8
Beta strandi117 – 125Combined sources9

3D structure databases

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

Sequence similaritiesi

Contains 1 CSD (cold-shock) domain.Curated

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
GeneTreeiENSGT00860000133704.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiP67809.
KOiK09276.
OMAiRRYPPYY.
PhylomeDBiP67809.
TreeFamiTF317306.

Family and domain databases

CDDicd04458. CSP_CDS. 1 hit.
InterProiIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

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

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.

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. 194 interactors.
DIPiDIP-29405N.
IntActiP67809. 312 interactors.
MINTiMINT-5001202.
STRINGi9606.ENSP00000361626.

PTM databases

iPTMnetiP67809.
PhosphoSitePlusiP67809.
SwissPalmiP67809.

Polymorphism and mutation databases

BioMutaiYBX1.
DMDMi54040031.

Proteomic databases

EPDiP67809.
MaxQBiP67809.
PaxDbiP67809.
PeptideAtlasiP67809.
PRIDEiP67809.
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.
GeneCardsiYBX1.
H-InvDBHIX0037767.
HIX0172381.
HGNCiHGNC:8014. YBX1.
HPAiCAB005875.
HPA040304.
HPA057159.
MIMi154030. gene.
neXtProtiNX_P67809.
OpenTargetsiENSG00000065978.
PharmGKBiPA31791.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
GeneTreeiENSGT00860000133704.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiP67809.
KOiK09276.
OMAiRRYPPYY.
PhylomeDBiP67809.
TreeFamiTF317306.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000065978-MONOMER.
ReactomeiR-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.
SignaLinkiP67809.
SIGNORiP67809.

Miscellaneous databases

ChiTaRSiYBX1. human.
EvolutionaryTraceiP67809.
GeneWikiiY_box_binding_protein_1.
GenomeRNAii4904.
PMAP-CutDBP67809.
PROiP67809.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000065978.
CleanExiHS_YBX1.
ExpressionAtlasiP67809. baseline and differential.
GenevisibleiP67809. HS.

Family and domain databases

CDDicd04458. CSP_CDS. 1 hit.
InterProiIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYBOX1_HUMAN
AccessioniPrimary (citable) accession number: P67809
Secondary accession number(s): P16990
, P16991, Q14972, Q15325, Q5FVF0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: January 23, 2007
Last modified: November 30, 2016
This is version 148 of the entry and version 3 of the sequence. [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
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.