YBOX1_RAT
ID YBOX1_RAT Reviewed; 322 AA.
AC P62961; P22568; P27817; P43482; Q4KMA4;
DT 31-AUG-2004, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Y-box-binding protein 1 {ECO:0000303|PubMed:1967130};
DE Short=YB-1 {ECO:0000303|PubMed:1967130};
DE AltName: Full=Enhancer factor I subunit A {ECO:0000303|PubMed:1967130};
DE Short=EFI-A {ECO:0000303|PubMed:1967130};
DE AltName: Full=Nuclease-sensitive element-binding protein 1;
DE AltName: Full=Y-box transcription factor;
GN Name=Ybx1 {ECO:0000312|RGD:61843};
GN Synonyms=Yb1 {ECO:0000303|PubMed:1967130};
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC TISSUE=Liver;
RX PubMed=1967130; DOI=10.1016/s0021-9258(18)45682-7;
RA Ozer J., Faber M., Chalkley R., Sealy L.;
RT "Isolation and characterization of a cDNA clone for the CCAAT transcription
RT factor EFIA reveals a novel structural motif.";
RL J. Biol. Chem. 265:22143-22152(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Petty K.J., Bartalena L., Nikodem V.M.;
RL Submitted (JUN-1991) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Ogawa H., Date T., Nishizawa M., Pitot H.C., Fujioka M.;
RL Submitted (OCT-1992) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Heart, and Lung;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
CC -!- FUNCTION: DNA- and RNA-binding protein involved in various processes,
CC such as translational repression, RNA stabilization, mRNA splicing, DNA
CC repair and transcription regulation. Predominantly acts as a RNA-
CC binding protein: binds preferentially to the 5'-[CU]CUGCG-3' RNA motif
CC and specifically recognizes mRNA transcripts modified by C5-
CC methylcytosine (m5C). Promotes mRNA stabilization: acts by binding to
CC m5C-containing mRNAs and recruiting the mRNA stability maintainer
CC ELAVL1, thereby preventing mRNA decay. Component of the CRD-mediated
CC complex that promotes MYC mRNA stability (By similarity). Contributes
CC to the regulation of translation by modulating the interaction between
CC the mRNA and eukaryotic initiation factors (By similarity). Plays a key
CC role in RNA composition of extracellular exosomes by defining the
CC sorting of small non-coding RNAs, such as tRNAs, Y RNAs, Vault RNAs and
CC miRNAs. Probably sorts RNAs in exosomes by recognizing and binding C5-
CC methylcytosine (m5C)-containing RNAs. Acts as a key effector of
CC epidermal progenitors by preventing epidermal progenitor senescence:
CC acts by regulating the translation of a senescence-associated subset of
CC cytokine mRNAs, possibly by binding to m5C-containing mRNAs. Also
CC involved in pre-mRNA alternative splicing regulation: binds to splice
CC sites in pre-mRNA and regulates splice site selection. Also able to
CC bind DNA: regulates transcription of the multidrug resistance gene MDR1
CC is enhanced in presence of the APEX1 acetylated form at 'Lys-6' and
CC 'Lys-7'. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'),
CC such as MDR1 and HLA class II genes. Promotes separation of DNA strands
CC that contain mismatches or are modified by cisplatin. Has
CC endonucleolytic activity and can introduce nicks or breaks into double-
CC stranded DNA, suggesting a role in DNA repair. The secreted form acts
CC as an extracellular mitogen and stimulates cell migration and
CC proliferation (By similarity). {ECO:0000250|UniProtKB:P67809,
CC ECO:0000250|UniProtKB:Q28618}.
CC -!- SUBUNIT: Homodimer in the presence of ATP. Component of the coding
CC region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU,
CC IGF2BP1, SYNCRIP and YBX1. Identified in a IGF2BP1-dependent mRNP
CC granule complex containing untranslated mRNAs. Component of the U11/U12
CC snRNPs that are part of the U12-type spliceosome (By similarity).
CC Identified in a histone pre-mRNA complex, at least composed of ERI1,
CC LSM11, SLBP, SNRPB, SYNCRIP and YBX1 (By similarity). Interacts with
CC IGF2BP1 and RBBP6. Component of cytoplasmic messenger ribonucleoprotein
CC particles (mRNPs). Interacts with AKT1, MBNL1, SFRS9, SFRS12,
CC ALYREF/THOC4, MSH2, XRCC5, WRN and NCL. Interacts (via C-terminus) with
CC APEX1 (via N-terminus); the interaction is increased with APEX1
CC acetylated at 'Lys-6' and 'Lys-7'. Interacts with AGO1 and AGO2.
CC Interacts with ANKRD2. Interacts with DERA (By similarity). Interacts
CC with FMR1; this interaction occurs in association with polyribosome.
CC Interacts with ZBTB7B (By similarity). Interacts with HDGF. Interacts
CC with ELAVL1; leading to ELAVL1 recruitment on C5-methylcytosine (m5C)-
CC containing mRNAs and subsequent mRNA stability (By similarity).
CC {ECO:0000250|UniProtKB:P62960, ECO:0000250|UniProtKB:P67809}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P67809}. Nucleus
CC {ECO:0000250|UniProtKB:P67809}. Cytoplasmic granule
CC {ECO:0000250|UniProtKB:P67809}. Secreted
CC {ECO:0000250|UniProtKB:P67809}. Secreted, extracellular exosome
CC {ECO:0000250|UniProtKB:P67809}. Note=Predominantly cytoplasmic in
CC proliferating cells. Cytotoxic stress and DNA damage enhance
CC translocation to the nucleus. Localized in cytoplasmic mRNP granules
CC containing untranslated mRNAs. Shuttles between nucleus and cytoplasm.
CC Localized with DDX1, MBNL1 and TIAL1 in stress granules upon stress.
CC Secreted by mesangial and monocytic cells after inflammatory
CC challenges. {ECO:0000250|UniProtKB:P67809}.
CC -!- DOMAIN: In the CSD domain, Trp-63 specifically recognizes C5-
CC methylcytosine (m5C) modification through its indole ring.
CC {ECO:0000250|UniProtKB:P67809}.
CC -!- PTM: Ubiquitinated by RBBP6; leading to a decrease of YBX1
CC transcactivational ability. {ECO:0000250|UniProtKB:P67809}.
CC -!- PTM: In the absence of phosphorylation the protein is retained in the
CC cytoplasm. {ECO:0000250|UniProtKB:P67809}.
CC -!- PTM: Cleaved by a 20S proteasomal protease in response to agents that
CC damage DNA. Cleavage takes place in the absence of ubiquitination and
CC ATP. The resulting N-terminal fragment accumulates in the nucleus (By
CC similarity). {ECO:0000250|UniProtKB:Q28618}.
CC -!- SIMILARITY: Belongs to the YBX1 family. {ECO:0000305}.
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DR EMBL; M57299; AAA41108.1; -; mRNA.
DR EMBL; M69138; AAA40906.1; -; mRNA.
DR EMBL; D13309; BAA02569.1; -; mRNA.
DR EMBL; BC072486; AAH72486.1; -; mRNA.
DR EMBL; BC098672; AAH98672.1; -; mRNA.
DR PIR; A23677; A23677.
DR RefSeq; NP_113751.3; NM_031563.3.
DR AlphaFoldDB; P62961; -.
DR BMRB; P62961; -.
DR SMR; P62961; -.
DR BioGRID; 271846; 6.
DR IntAct; P62961; 9.
DR MINT; P62961; -.
DR STRING; 10116.ENSRNOP00000055494; -.
DR iPTMnet; P62961; -.
DR PhosphoSitePlus; P62961; -.
DR jPOST; P62961; -.
DR PaxDb; P62961; -.
DR PRIDE; P62961; -.
DR GeneID; 500538; -.
DR KEGG; rno:500538; -.
DR UCSC; RGD:61843; rat.
DR CTD; 4904; -.
DR RGD; 61843; Ybx1.
DR eggNOG; KOG3070; Eukaryota.
DR InParanoid; P62961; -.
DR PhylomeDB; P62961; -.
DR Reactome; R-RNO-72163; mRNA Splicing - Major Pathway.
DR Reactome; R-RNO-72165; mRNA Splicing - Minor Pathway.
DR Reactome; R-RNO-9017802; Noncanonical activation of NOTCH3.
DR PRO; PR:P62961; -.
DR Proteomes; UP000002494; Unplaced.
DR GO; GO:0070937; C:CRD-mediated mRNA stability complex; ISO:RGD.
DR GO; GO:0005737; C:cytoplasm; IDA:RGD.
DR GO; GO:0010494; C:cytoplasmic stress granule; ISS:UniProtKB.
DR GO; GO:0030425; C:dendrite; IDA:RGD.
DR GO; GO:0070062; C:extracellular exosome; ISS:UniProtKB.
DR GO; GO:0071204; C:histone pre-mRNA 3'end processing complex; ISS:UniProtKB.
DR GO; GO:1990124; C:messenger ribonucleoprotein complex; IDA:RGD.
DR GO; GO:0043025; C:neuronal cell body; IDA:RGD.
DR GO; GO:0005634; C:nucleus; IDA:RGD.
DR GO; GO:0048471; C:perinuclear region of cytoplasm; IDA:RGD.
DR GO; GO:1990904; C:ribonucleoprotein complex; ISS:UniProtKB.
DR GO; GO:0005689; C:U12-type spliceosomal complex; ISO:RGD.
DR GO; GO:0062153; F:C5-methylcytidine-containing RNA binding; ISS:UniProtKB.
DR GO; GO:0003682; F:chromatin binding; ISO:RGD.
DR GO; GO:0051020; F:GTPase binding; ISO:RGD.
DR GO; GO:0035198; F:miRNA binding; ISS:UniProtKB.
DR GO; GO:0003729; F:mRNA binding; IPI:RGD.
DR GO; GO:0003676; F:nucleic acid binding; IBA:GO_Central.
DR GO; GO:0002039; F:p53 binding; IMP:RGD.
DR GO; GO:0003723; F:RNA binding; IDA:RGD.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:RGD.
DR GO; GO:1990837; F:sequence-specific double-stranded DNA binding; ISO:RGD.
DR GO; GO:0003697; F:single-stranded DNA binding; IDA:RGD.
DR GO; GO:0098761; P:cellular response to interleukin-7; ISO:RGD.
DR GO; GO:0070934; P:CRD-mediated mRNA stabilization; ISS:UniProtKB.
DR GO; GO:0048598; P:embryonic morphogenesis; ISS:UniProtKB.
DR GO; GO:0008544; P:epidermis development; ISS:UniProtKB.
DR GO; GO:0001701; P:in utero embryonic development; ISO:RGD.
DR GO; GO:1990428; P:miRNA transport; ISS:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0048255; P:mRNA stabilization; ISS:UniProtKB.
DR GO; GO:0043066; P:negative regulation of apoptotic process; IDA:RGD.
DR GO; GO:2000773; P:negative regulation of cellular senescence; ISS:UniProtKB.
DR GO; GO:0046627; P:negative regulation of insulin receptor signaling pathway; IMP:RGD.
DR GO; GO:1900152; P:negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay; ISO:RGD.
DR GO; GO:0051154; P:negative regulation of striated muscle cell differentiation; ISO:RGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IDA:RGD.
DR GO; GO:0017148; P:negative regulation of translation; ISS:UniProtKB.
DR GO; GO:0051781; P:positive regulation of cell division; IEA:UniProtKB-KW.
DR GO; GO:0008284; P:positive regulation of cell population proliferation; IMP:RGD.
DR GO; GO:2000767; P:positive regulation of cytoplasmic translation; ISO:RGD.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:RGD.
DR GO; GO:1903608; P:protein localization to cytoplasmic stress granule; ISO:RGD.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; ISO:RGD.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR GO; GO:0050658; P:RNA transport; ISS:UniProtKB.
DR GO; GO:0051031; P:tRNA transport; ISS:UniProtKB.
DR CDD; cd04458; CSP_CDS; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR011129; CSD.
DR InterPro; IPR019844; CSD_1.
DR InterPro; IPR002059; CSP_DNA-bd.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF00313; CSD; 1.
DR PRINTS; PR00050; COLDSHOCK.
DR SMART; SM00357; CSP; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR PROSITE; PS00352; CSD_1; 1.
DR PROSITE; PS51857; CSD_2; 1.
PE 2: Evidence at transcript level;
KW Acetylation; Activator; Cytoplasm; DNA-binding; Isopeptide bond; Mitogen;
KW mRNA processing; mRNA splicing; Nucleus; Phosphoprotein;
KW Reference proteome; Repressor; RNA-binding; Secreted; Transcription;
KW Transcription regulation; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT CHAIN 2..322
FT /note="Y-box-binding protein 1"
FT /id="PRO_0000100221"
FT DOMAIN 59..123
FT /note="CSD"
FT REGION 1..47
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 14..69
FT /note="Interaction with ss-DNA"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT REGION 63..68
FT /note="C5-methylcytosine binding"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT REGION 118..322
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 154..179
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 248..267
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 286..304
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 63
FT /note="Important for C5-methylcytosine-recognition"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT SITE 217..218
FT /note="Cleavage; by 20S proteasomal protease"
FT /evidence="ECO:0000250|UniProtKB:Q28618"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 100
FT /note="Phosphoserine; by PKB/AKT1"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 160
FT /note="Phosphotyrosine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 163
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 165
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 172
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 174
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 299
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 302
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT MOD_RES 312
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT CROSSLNK 24
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT CROSSLNK 135
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT /evidence="ECO:0000250|UniProtKB:P67809"
FT CONFLICT 5
FT /note="A -> P (in Ref. 2; AAA40906)"
FT /evidence="ECO:0000305"
FT CONFLICT 306
FT /note="P -> S (in Ref. 1; AAA41108)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 322 AA; 35730 MW; C6667CF7CA10D45D CRC64;
MSSEAETQQP PAAPAAALSA ADTKPGSTGS GAGSGGPGGL TSAAPAGGDK KVIATKVLGT
VKWFNVRNGY GFINRNDTKE DVFVHQTAIK KNNPRKYLRS VGDGETVEFD VVEGEKGAEA
ANVTGPGGVP VQGSKYAADR NHYRRYPRRR GPPRNYQQNY QNSESGEKNE GSESAPEGQA
QQRRPYRRRR FPPYYMRRPY ARRPQYSNPP VQGEVMEGAD NQGAGEQGRP VRQNMYRGYR
PRFRRGPPRQ RQPREDGNEE DKENQGDETQ GQQPPQRRYR RNFNYRRRRP ENPKPQDGKE
TKAADPPAEN SSAPEAEQGG AE
