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Protein

Nuclease-sensitive element-binding protein 1

Gene

YBX1

Organism
Oryctolagus cuniculus (Rabbit)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Mediates pre-mRNA alternative splicing regulation. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'). 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. Component of the CRD-mediated complex that promotes MYC mRNA stability. Binds to splice sites in pre-mRNA and regulates splice site selection. 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 preferentially to the 5'-[CU]CUGCG-3' motif in vitro (By similarity). Binds and stabilizes cytoplasmic mRNA. Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors.By similarity4 Publications
The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.By similarity

GO - Molecular functioni

GO - Biological processi

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

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
Enhancer factor I subunit A
Short name:
EFI-A
Y-box transcription factor
Y-box-binding protein 1
Short name:
YB-1
p50
Gene namesi
Name:YBX1
Synonyms:NSEP1, YB1
OrganismiOryctolagus cuniculus (Rabbit)
Taxonomic identifieri9986 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresLagomorphaLeporidaeOryctolagus
Proteomesi
  • UP000001811 Componenti: Unplaced

Subcellular locationi

  • Cytoplasm
  • Nucleus
  • Cytoplasmic granule
  • Secreted By similarity

  • Note: Localized with DDX1, MBNL1 and TIAL1 in stress granules upon stress. Secreted by mesangial and monocytic cells after inflammatory challenges (By similarity). Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in proliferating cells. Cytotoxic stress and DNA damage enhance translocation to the nucleus. Localized in cytoplasmic mRNP granules containing untranslated mRNAs.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Secreted

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi102 – 1021S → A: Abolishes phosphorylation by PKB/AKT1. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 324323Nuclease-sensitive element-binding protein 1PRO_0000227814Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei102 – 1021Phosphoserine; by PKB/AKT11 Publication
Cross-linki137 – 137Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei162 – 1621PhosphotyrosineBy similarity
Modified residuei165 – 1651PhosphoserineBy similarity
Modified residuei167 – 1671PhosphoserineBy similarity
Modified residuei174 – 1741PhosphoserineBy similarity
Modified residuei176 – 1761PhosphoserineBy similarity
Modified residuei301 – 3011N6-acetyllysineBy similarity
Modified residuei304 – 3041N6-acetyllysineBy similarity
Modified residuei314 – 3141PhosphoserineBy similarity

Post-translational modificationi

Ubiquitinated by RBBP6; leading to a decrease of YBX1 transcactivational ability.By similarity
In the absence of phosphorylation the protein is retained in the cytoplasm (By similarity). Phosphorylation by PKB/AKT1 reduces interaction with cytoplasmic mRNA.By similarity1 Publication
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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei219 – 2202Cleavage; by 20S proteasomal proteaseBy similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

PTM databases

iPTMnetiQ28618.

Interactioni

Subunit structurei

Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1. Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1. Identification in a mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. Interacts with AKT1, MBNL1, IGF2BP1, SFRS9, ALYREF/THOC4, MSH2, XRCC5, RBBP6, WRN and NCL. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. 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. Can form heterotrimer with PURA and PURB. 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 (By similarity). Component of cytoplasmic messenger ribonucleoprotein particles (mRNPs). Interacts with FMR1; this interaction occurs in association with polyribosome (By similarity).By similarity2 Publications

Protein-protein interaction databases

BioGridi1172602. 2 interactions.
STRINGi9986.ENSOCUP00000019994.

Structurei

3D structure databases

ProteinModelPortaliQ28618.
SMRiQ28618. Positions 52-129.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini58 – 12871CSDAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni15 – 7157Interaction with ss-DNABy similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi185 – 291107Arg-richAdd
BLAST

Sequence similaritiesi

Contains 1 CSD (cold-shock) domain.Curated

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiQ28618.
KOiK09276.

Family and domain databases

Gene3Di2.40.50.140. 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.

Q28618-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSEAETQQP PAAPPAAPAL SAAETKPGTT 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 TQGQQPPPSR YRRNFNYRRR RPDNPKPQDG
310 320
KETKAADPPA ENSSAPEAEQ GGAE
Length:324
Mass (Da):35,824
Last modified:January 23, 2007 - v3
Checksum:iB2700FD2E61BF8B9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U16821 mRNA. Translation: AAA66069.1.
PIRiA55971.
RefSeqiNP_001076254.1. NM_001082785.1.
UniGeneiOcu.6201.

Genome annotation databases

GeneIDi100009583.
KEGGiocu:100009583.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U16821 mRNA. Translation: AAA66069.1.
PIRiA55971.
RefSeqiNP_001076254.1. NM_001082785.1.
UniGeneiOcu.6201.

3D structure databases

ProteinModelPortaliQ28618.
SMRiQ28618. Positions 52-129.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi1172602. 2 interactions.
STRINGi9986.ENSOCUP00000019994.

PTM databases

iPTMnetiQ28618.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100009583.
KEGGiocu:100009583.

Organism-specific databases

CTDi4904.

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiQ28618.
KOiK09276.

Family and domain databases

Gene3Di2.40.50.140. 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...

Publicationsi

  1. "The major protein of messenger ribonucleoprotein particles in somatic cells is a member of the Y-box binding transcription factor family."
    Evdokimova V.M., Wei C.L., Sitikov A.S., Simonenko P.N., Lazarev O.A., Vasilenko K.S., Ustinov V.A., Hershey J.W., Ovchinnikov L.P.
    J. Biol. Chem. 270:3186-3192(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, SUBCELLULAR LOCATION.
    Tissue: Bone marrow.
  2. "Proteasome-mediated cleavage of the Y-box-binding protein 1 is linked to DNA-damage stress response."
    Sorokin A.V., Selyutina A.A., Skabkin M.A., Guryanov S.G., Nazimov I.V., Richard C., Th'ng J., Yau J., Sorensen P.H.B., Ovchinnikov L.P., Evdokimova V.
    EMBO J. 24:3602-3612(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE, PROTEOLYTIC CLEAVAGE BY 20S PROTEASOMAL PROTEASE, SUBCELLULAR LOCATION.
  3. "The major mRNA-associated protein YB-1 is a potent 5' cap-dependent mRNA stabilizer."
    Evdokimova V., Ruzanov P., Imataka H., Raught B., Svitkin Y., Ovchinnikov L.P., Sonenberg N.
    EMBO J. 20:5491-5502(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  4. "The mRNA-binding protein YB-1 (p50) prevents association of the eukaryotic initiation factor eIF4G with mRNA and inhibits protein synthesis at the initiation stage."
    Nekrasov M.P., Ivshina M.P., Chernov K.G., Kovrigina E.A., Evdokimova V.M., Thomas A.A.M., Hershey J.W.B., Ovchinnikov L.P.
    J. Biol. Chem. 278:13936-13943(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT, SUBCELLULAR LOCATION.
  5. Cited for: MUTAGENESIS OF SER-102, PHOSPHORYLATION AT SER-102, SUBCELLULAR LOCATION, INTERACTION WITH AKT1, FUNCTION.

Entry informationi

Entry nameiYBOX1_RABIT
AccessioniPrimary (citable) accession number: Q28618
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: January 23, 2007
Last modified: July 6, 2016
This is version 111 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. 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.