P62961 (YBOX1_RAT) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	Ybx1
Synonyms:	Msy-1, Nsep1, Yb1

Organism

Rattus norvegicus (Rat) [Reference proteome]

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	322 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation By similarity.
Subunit structure	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 mRNP granule complex, at least composed of ACTB, ACTN4, DHX9, ERG, HNRNPA1, HNRNPA2B1, HNRNPAB, HNRNPD, HNRNPL, HNRNPR, HNRNPU, HSPA1, HSPA8, IGF2BP1, ILF2, ILF3, NCBP1, NCL, PABPC1, PABPC4, PABPN1, RPLP0, RPS3, RPS3A, RPS4X, RPS8, RPS9, SYNCRIP, TROVE2, YBX1 and 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 EIF2C1 and EIF2C2 By similarity.
Subcellular location	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.
Post-translational modification	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.
Sequence similarities	Contains 1 CSD (cold-shock) domain.

Ontologies

Keywords
Biological process	Transcription Transcription regulation mRNA processing mRNA splicing
Cellular component	Cytoplasm Nucleus Secreted
Ligand	DNA-binding RNA-binding
Molecular function	Activator Mitogen Repressor
PTM	Acetylation Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	CRD-mediated mRNA stabilization Inferred from sequence or structural similarity. Source: UniProtKB RNA splicing Inferred from electronic annotation. Source: UniProtKB-KW mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW negative regulation of apoptotic process Inferred from direct assay PubMed 16158057. Source: RGD negative regulation of insulin receptor signaling pathway Inferred from mutant phenotype PubMed 12554649. Source: RGD negative regulation of transcription from RNA polymerase II promoter Inferred from direct assay PubMed 12835324. Source: RGD positive regulation of cell division Inferred from electronic annotation. Source: UniProtKB-KW positive regulation of cell proliferation Inferred from mutant phenotype PubMed 15615704. Source: RGD positive regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 15615704. Source: RGD transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasmic stress granule Inferred from sequence or structural similarity. Source: UniProtKB dendrite Inferred from direct assay PubMed 14559349. Source: RGD extracellular region Inferred from electronic annotation. Source: UniProtKB-SubCell histone pre-mRNA 3'end processing complex Inferred from sequence or structural similarity. Source: UniProtKB perinuclear region of cytoplasm Inferred from direct assay PubMed 16002047. Source: RGD
Molecular_function	mRNA binding Inferred from physical interaction PubMed 16508950. Source: RGD p53 binding Inferred from mutant phenotype PubMed 16158057. Source: RGD sequence-specific DNA binding Inferred from direct assay PubMed 16278212. Source: RGD single-stranded DNA binding Inferred from direct assay PubMed 17893273. Source: RGD
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Initiator methionine	1	1	Removed By similarity
	Chain	2 – 322	321	Nuclease-sensitive element-binding protein 1		PRO_0000100221
Regions
	Domain	59 – 123	65	CSD
	Region	14 – 69	56	Interaction with ss-DNA By similarity
Sites
	Site	217 – 218	2	Cleavage; by 20S proteasomal protease By similarity
Amino acid modifications
	Modified residue	2	1	N-acetylserine By similarity
	Modified residue	100	1	Phosphoserine; by PKB/AKT1 Ref.5
	Modified residue	160	1	Phosphotyrosine By similarity
	Modified residue	163	1	Phosphoserine By similarity
	Modified residue	165	1	Phosphoserine By similarity
	Modified residue	172	1	Phosphoserine By similarity
	Modified residue	174	1	Phosphoserine By similarity
	Modified residue	299	1	N6-acetyllysine By similarity
	Modified residue	302	1	N6-acetyllysine By similarity
	Modified residue	312	1	Phosphoserine Ref.5
	Cross-link	135		Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity
Experimental info
	Sequence conflict	5	1	A → P in AAA40906. Ref.2
	Sequence conflict	306	1	P → S in AAA41108. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	P62961 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: C6667CF7CA10D45D	FASTA	322	35,730
	10 20 30 40 50 60 MSSEAETQQP PAAPAAALSA ADTKPGSTGS GAGSGGPGGL TSAAPAGGDK KVIATKVLGT 70 80 90 100 110 120 VKWFNVRNGY GFINRNDTKE DVFVHQTAIK KNNPRKYLRS VGDGETVEFD VVEGEKGAEA 130 140 150 160 170 180 ANVTGPGGVP VQGSKYAADR NHYRRYPRRR GPPRNYQQNY QNSESGEKNE GSESAPEGQA 190 200 210 220 230 240 QQRRPYRRRR FPPYYMRRPY ARRPQYSNPP VQGEVMEGAD NQGAGEQGRP VRQNMYRGYR 250 260 270 280 290 300 PRFRRGPPRQ RQPREDGNEE DKENQGDETQ GQQPPQRRYR RNFNYRRRRP ENPKPQDGKE 310 320 TKAADPPAEN SSAPEAEQGG AE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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.
[5]	"Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites." Hoffert J.D., Pisitkun T., Wang G., Shen R.-F., Knepper M.A. Proc. Natl. Acad. Sci. U.S.A. 103:7159-7164(2006) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-100 AND SER-312, MASS SPECTROMETRY. Tissue: Renal collecting duct.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
IPI	IPI00551815.
PIR	A23677.
RefSeq	NP_113751.3. NM_031563.3.
UniGene	Rn.110976. Rn.194909.
3D structure databases
ProteinModelPortal	P62961.
SMR	P62961. Positions 50-127.
ModBase	Search...
Protein-protein interaction databases
IntAct	P62961. 2 interactions.
MINT	MINT-157738.
STRING	10116.ENSRNOP00000055494.
PTM databases
PhosphoSite	P62961.
Proteomic databases
PaxDb	P62961.
PRIDE	P62961.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	500538.
KEGG	rno:500538.
UCSC	RGD:61843. rat.
Organism-specific databases
CTD	4904.
RGD	61843. Ybx1.
Phylogenomic databases
eggNOG	COG1278.
HOGENOM	HOG000116439.
HOVERGEN	HBG008757.
InParanoid	P62961.
KO	K09276.
OrthoDB	EOG46DM3W.
Gene expression databases
ArrayExpress	P62961.
Genevestigator	P62961.
GermOnline	ENSRNOG00000032902. Rattus norvegicus.
Family and domain databases
Gene3D	2.40.50.140. 1 hit.
InterPro	IPR019844. Cold-shock_CS. IPR011129. Cold_shock_prot. IPR002059. CSP_DNA-bd. IPR012340. NA-bd_OB-fold. [Graphical view]
Pfam	PF00313. CSD. 1 hit. [Graphical view]
PRINTS	PR00050. COLDSHOCK.
SMART	SM00357. CSP. 1 hit. [Graphical view]
SUPFAM	SSF50249. Nucleic_acid_OB. 1 hit.
PROSITE	PS00352. COLD_SHOCK. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	302963.

Entry information

Entry name

YBOX1_RAT

Accession

Primary (citable) accession number: P62961
Secondary accession number(s): P22568 , P27817, P43482, Q4KMA4

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 31, 2004
Last sequence update:	January 23, 2007
Last modified:	May 29, 2013
This is version 91 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program