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
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein 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' and 'Lys-7'. Binds preferentially to 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

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-MMU-72163 mRNA Splicing - Major Pathway
R-MMU-72165 mRNA Splicing - Minor Pathway
R-MMU-9017802 Noncanonical activation of NOTCH3

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, Msy1, Nsep1, Yb1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 4

Organism-specific databases

MGIiMGI:99146 Ybx1

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00001002202 – 322Nuclease-sensitive element-binding protein 1Add BLAST321

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Cross-linki24Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei100Phosphoserine; by PKB/AKT1By similarity1
Cross-linki135Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei160PhosphotyrosineBy similarity1
Modified residuei163PhosphoserineCombined sources1
Modified residuei165PhosphoserineBy similarity1
Modified residuei172PhosphoserineCombined sources1
Modified residuei174PhosphoserineCombined sources1
Modified residuei299N6-acetyllysineBy similarity1
Modified residuei302N6-acetyllysineBy similarity1
Modified residuei312PhosphoserineCombined sources1

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)DescriptionActionsGraphical viewLength
Sitei217 – 218Cleavage; by 20S proteasomal proteaseBy similarity2

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiP62960
PaxDbiP62960
PeptideAtlasiP62960
PRIDEiP62960

PTM databases

iPTMnetiP62960
PhosphoSitePlusiP62960
SwissPalmiP62960

Expressioni

Tissue specificityi

Expressed at high levels in the testis. Present in the mRNP particles that mediate the storage and masking of mRNAs during spermiogenesis.1 Publication

Developmental stagei

Found at very low levels at day 10 and levels increase at day 15 and persist throughout adulthood.1 Publication

Gene expression databases

BgeeiENSMUSG00000028639
CleanExiMM_YBX1
ExpressionAtlasiP62960 baseline and differential
GenevisibleiP62960 MM

Interactioni

Subunit structurei

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 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. 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 (By similarity). Interacts with ANKRD2 (By similarity). Interacts with DERA (By similarity). Can form heterotrimer with PURA and PURB. Identified in a histone pre-mRNA complex, at least composed of ERI1, LSM11, SLBP, SNRPB, SYNCRIP and YBX1. Interacts with FMR1; this interaction occurs in association with polyribosome (PubMed:11162447). Interacts with ZBTB7B (PubMed:28784777).By similarity5 Publications

GO - Molecular functioni

Protein-protein interaction databases

BioGridi204613, 62 interactors
DIPiDIP-34256N
IntActiP62960, 74 interactors
MINTiP62960
STRINGi10090.ENSMUSP00000078589

Structurei

3D structure databases

ProteinModelPortaliP62960
SMRiP62960
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini59 – 123CSDAdd BLAST65

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni16 – 69Interaction with ss-DNABy similarityAdd BLAST54

Phylogenomic databases

eggNOGiKOG3070 Eukaryota
COG1278 LUCA
GeneTreeiENSGT00880000137907
HOGENOMiHOG000116439
HOVERGENiHBG008757
InParanoidiP62960
KOiK09276
OMAiRRYPPYY
OrthoDBiEOG091G0W9A
PhylomeDBiP62960
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

Sequencei

Sequence statusi: Complete.

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

P62960-1 [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)DescriptionActionsGraphical viewLength
Sequence conflicti29G → A in AAA63390 (PubMed:1622927).Curated1
Sequence conflicti43 – 45AAP → RR in CAA40847 (PubMed:1741293).Curated3
Sequence conflicti238G → P in CAA40847 (PubMed:1741293).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M60419 mRNA Translation: AAA40577.1
M62867 mRNA Translation: AAA63390.1
X57621 mRNA Translation: CAA40847.1
BC013450 mRNA Translation: AAH13450.1
BC013620 mRNA Translation: AAH13620.1
BC029747 mRNA Translation: AAH29747.1
BC031472 mRNA Translation: AAH31472.1
BC061634 mRNA Translation: AAH61634.1
CCDSiCCDS18579.1
PIRiI58195
RefSeqiNP_035862.2, NM_011732.2
UniGeneiMm.258204

Genome annotation databases

EnsembliENSMUST00000079644; ENSMUSP00000078589; ENSMUSG00000028639
GeneIDi22608
KEGGimmu:22608
UCSCiuc008ulu.1 mouse

Similar proteinsi

Entry informationi

Entry nameiYBOX1_MOUSE
AccessioniPrimary (citable) accession number: P62960
Secondary accession number(s): P22568, P27817, P43482
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: January 23, 2007
Last modified: May 23, 2018
This is version 147 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot

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
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health