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Protein

Nuclease-sensitive element-binding protein 1

Gene

Ybx1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Mediates pre-mRNA alternative splicing regulation. Component of the CRD-mediated complex that promotes MYC mRNA stability. 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. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as HLA class II genes. 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. Its transcriptional activity on the multidrug resistance gene MDR1 is enhanced in presence of the APEX1 acetylated form at 'Lys-6'. Binds preferentially to the 5'-[CU]CUGCG-3' motif in vitro (By similarity).By similarity
The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.By similarity

GO - Molecular functioni

  • mRNA binding Source: RGD
  • p53 binding Source: RGD
  • RNA binding Source: UniProtKB
  • sequence-specific DNA binding Source: RGD
  • single-stranded DNA binding Source: RGD
  • transcription factor binding Source: RGD

GO - Biological processi

  • CRD-mediated mRNA stabilization Source: UniProtKB
  • mRNA processing Source: UniProtKB-KW
  • negative regulation of apoptotic process Source: RGD
  • negative regulation of insulin receptor signaling pathway Source: RGD
  • negative regulation of transcription from RNA polymerase II promoter Source: RGD
  • positive regulation of cell division Source: UniProtKB-KW
  • positive regulation of cell proliferation Source: RGD
  • positive regulation of transcription from RNA polymerase II promoter Source: RGD
  • RNA splicing Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW
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
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:Msy-1, Nsep1, Yb1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi61843. Ybx1.

Subcellular locationi

  • Cytoplasm By similarity
  • Nucleus By similarity
  • Cytoplasmic granule By similarity
  • Secreted By similarity

  • Note: 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. Localized with DDX1, MBNL1 and TIAL1 in stress granules upon stress. Secreted by mesangial and monocytic cells after inflammatory challenges (By similarity).By similarity

GO - Cellular componenti

  • cytoplasm Source: RGD
  • cytoplasmic stress granule Source: UniProtKB
  • dendrite Source: RGD
  • extracellular region Source: UniProtKB-SubCell
  • histone pre-mRNA 3'end processing complex Source: UniProtKB
  • intracellular ribonucleoprotein complex Source: UniProtKB
  • messenger ribonucleoprotein complex Source: RGD
  • nucleus Source: RGD
  • perinuclear region of cytoplasm Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Secreted

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 322321Nuclease-sensitive element-binding protein 1PRO_0000100221Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity
Modified residuei100 – 1001Phosphoserine; by PKB/AKT1By similarity
Cross-linki135 – 135Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei160 – 1601PhosphotyrosineBy similarity
Modified residuei163 – 1631PhosphoserineBy similarity
Modified residuei165 – 1651PhosphoserineBy similarity
Modified residuei172 – 1721PhosphoserineBy similarity
Modified residuei174 – 1741PhosphoserineBy similarity
Modified residuei299 – 2991N6-acetyllysineBy similarity
Modified residuei302 – 3021N6-acetyllysineBy similarity
Modified residuei312 – 3121PhosphoserineBy 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
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)LengthDescriptionGraphical viewFeature identifierActions
Sitei217 – 2182Cleavage; by 20S proteasomal proteaseBy similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiP62961.
PRIDEiP62961.

PTM databases

iPTMnetiP62961.
PhosphoSiteiP62961.

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. Component of cytoplasmic messenger ribonucleoprotein particles (mRNPs). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Interacts with AKT1, MBNL1, IGF2BP1, SFRS9, ALYREF/THOC4, MSH2, XRCC5, RBBP6, 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. Can form heterotrimer with PURA and PURB. 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'. Interacts with AGO1 and AGO2. Interacts with ANKRD2. Interacts with DERA (By similarity). Interacts with FMR1; this interaction occurs in association with polyribosome (By similarity).By similarity

GO - Molecular functioni

  • p53 binding Source: RGD
  • transcription factor binding Source: RGD

Protein-protein interaction databases

BioGridi271846. 3 interactions.
IntActiP62961. 3 interactions.
MINTiMINT-157738.
STRINGi10116.ENSRNOP00000055494.

Structurei

3D structure databases

ProteinModelPortaliP62961.
SMRiP62961. Positions 50-127.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini59 – 12365CSDAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 6956Interaction with ss-DNABy similarityAdd
BLAST

Sequence similaritiesi

Contains 1 CSD (cold-shock) domain.Curated

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiP62961.
KOiK09276.
PhylomeDBiP62961.

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.

P62961-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSEAETQQP PAAPAAALSA ADTKPGSTGS GAGSGGPGGL TSAAPAGGDK
60 70 80 90 100
KVIATKVLGT VKWFNVRNGY GFINRNDTKE DVFVHQTAIK KNNPRKYLRS
110 120 130 140 150
VGDGETVEFD VVEGEKGAEA ANVTGPGGVP VQGSKYAADR NHYRRYPRRR
160 170 180 190 200
GPPRNYQQNY QNSESGEKNE GSESAPEGQA QQRRPYRRRR FPPYYMRRPY
210 220 230 240 250
ARRPQYSNPP VQGEVMEGAD NQGAGEQGRP VRQNMYRGYR PRFRRGPPRQ
260 270 280 290 300
RQPREDGNEE DKENQGDETQ GQQPPQRRYR RNFNYRRRRP ENPKPQDGKE
310 320
TKAADPPAEN SSAPEAEQGG AE
Length:322
Mass (Da):35,730
Last modified:January 23, 2007 - v3
Checksum:iC6667CF7CA10D45D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti5 – 51A → P in AAA40906 (Ref. 2) Curated
Sequence conflicti306 – 3061P → S in AAA41108 (PubMed:1967130).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57299 mRNA. Translation: AAA41108.1.
M69138 mRNA. Translation: AAA40906.1.
D13309 mRNA. Translation: BAA02569.1.
BC072486 mRNA. Translation: AAH72486.1.
BC098672 mRNA. Translation: AAH98672.1.
PIRiA23677.
RefSeqiNP_113751.3. NM_031563.3.
UniGeneiRn.110976.
Rn.194909.

Genome annotation databases

GeneIDi500538.
KEGGirno:500538.
UCSCiRGD:61843. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57299 mRNA. Translation: AAA41108.1.
M69138 mRNA. Translation: AAA40906.1.
D13309 mRNA. Translation: BAA02569.1.
BC072486 mRNA. Translation: AAH72486.1.
BC098672 mRNA. Translation: AAH98672.1.
PIRiA23677.
RefSeqiNP_113751.3. NM_031563.3.
UniGeneiRn.110976.
Rn.194909.

3D structure databases

ProteinModelPortaliP62961.
SMRiP62961. Positions 50-127.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi271846. 3 interactions.
IntActiP62961. 3 interactions.
MINTiMINT-157738.
STRINGi10116.ENSRNOP00000055494.

PTM databases

iPTMnetiP62961.
PhosphoSiteiP62961.

Proteomic databases

PaxDbiP62961.
PRIDEiP62961.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi500538.
KEGGirno:500538.
UCSCiRGD:61843. rat.

Organism-specific databases

CTDi4904.
RGDi61843. Ybx1.

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000116439.
HOVERGENiHBG008757.
InParanoidiP62961.
KOiK09276.
PhylomeDBiP62961.

Miscellaneous databases

PROiP62961.

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

« Hide 'large scale' publications
  1. "Isolation and characterization of a cDNA clone for the CCAAT transcription factor EFIA reveals a novel structural motif."
    Ozer J., Faber M., Chalkley R., Sealy L.
    J. Biol. Chem. 265:22143-22152(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Liver.
  2. Petty K.J., Bartalena L., Nikodem V.M.
    Submitted (JUN-1991) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  3. Ogawa H., Date T., Nishizawa M., Pitot H.C., Fujioka M.
    Submitted (OCT-1992) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  4. "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].
    Tissue: Heart and Lung.

Entry informationi

Entry nameiYBOX1_RAT
AccessioniPrimary (citable) accession number: P62961
Secondary accession number(s): P22568
, P27817, P43482, Q4KMA4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: January 23, 2007
Last modified: July 6, 2016
This is version 113 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, 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.