ID YBOX1_CHICK Reviewed; 321 AA. AC Q06066; DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot. DT 01-FEB-1994, sequence version 1. DT 24-JAN-2024, entry version 132. DE RecName: Full=Y-box-binding protein 1 {ECO:0000303|PubMed:8321222}; DE Short=YB-1 {ECO:0000303|PubMed:8321222}; DE AltName: Full=Y-box transcription factor; GN Name=YBX1 {ECO:0000250|UniProtKB:P67809}; GN Synonyms=YB1 {ECO:0000303|PubMed:8321222}; OS Gallus gallus (Chicken). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; OC Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; OC Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae; OC Phasianinae; Gallus. OX NCBI_TaxID=9031; RN [1] RP NUCLEOTIDE SEQUENCE [MRNA], AND FUNCTION. RC TISSUE=Embryonic liver; RX PubMed=8321222; DOI=10.1128/mcb.13.7.4186-4196.1993; RA Grant C.E., Deeley R.G.; RT "Cloning and characterization of chicken YB-1: regulation of expression in RT the liver."; RL Mol. Cell. Biol. 13:4186-4196(1993). CC -!- FUNCTION: DNA- and RNA-binding protein involved in various processes, CC such as translational repression, RNA stabilization, mRNA splicing and CC transcription regulation (PubMed:8321222). Binds preferentially to the CC 5'-[CU]CUGCG-3' RNA motif and specifically recognizes mRNA transcripts CC modified by C5-methylcytosine (m5C) (By similarity). Promotes mRNA CC stabilization: acts by binding to m5C-containing mRNAs and preventing CC mRNA decay (By similarity). Plays a role in the maternal-to-zygotic CC transition in early embryo by binding to m5C-containing maternal mRNAs CC and preventing their degradation (By similarity). Also promotes CC maternal-to-zygotic transition in oocytes and embryos by promoting CC translation repression; molecular mechanisms governing translation CC repression are unknown (By similarity). Plays a key role in RNA CC composition of extracellular exosomes by defining the sorting of small CC non-coding RNAs, such as tRNAs, Y RNAs, Vault RNAs and miRNAs (By CC similarity). Probably sorts RNAs in exosomes by recognizing and binding CC C5-methylcytosine (m5C)-containing RNAs (By similarity). Acts as a key CC effector of epidermal progenitors by preventing epidermal progenitor CC senescence: acts by regulating the translation of a senescence- CC associated subset of cytokine mRNAs, possibly by binding to m5C- CC containing mRNAs (By similarity). Also involved in pre-mRNA alternative CC splicing regulation: binds to splice sites in pre-mRNA and regulates CC splice site selection (By similarity). Also able to bind DNA and CC regulate transcription (PubMed:8321222). Binds to promoters that CC contain a Y-box (5'-CTGATTGGCCAA-3') (By similarity). Promotes CC separation of DNA strands that contain mismatches or are modified by CC cisplatin (By similarity). Has endonucleolytic activity and can CC introduce nicks or breaks into double-stranded DNA, suggesting a role CC in DNA repair (By similarity). The secreted form acts as an CC extracellular mitogen and stimulates cell migration and proliferation CC (By similarity). {ECO:0000250|UniProtKB:B5DE31, CC ECO:0000250|UniProtKB:P67809, ECO:0000269|PubMed:8321222}. 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}. Cytoplasm, P-body CC {ECO:0000250|UniProtKB:P62960}. CC -!- DOMAIN: In the CSD domain, Trp-62 specifically recognizes C5- CC methylcytosine (m5C) modification through its indole ring. CC {ECO:0000250|UniProtKB:P67809}. CC -!- SIMILARITY: Belongs to the YBX1 family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; L13032; AAA02573.1; -; mRNA. DR PIR; A48136; A48136. DR AlphaFoldDB; Q06066; -. DR SMR; Q06066; -. DR STRING; 9031.ENSGALP00000054264; -. DR PaxDb; 9031-ENSGALP00000028616; -. DR VEuPathDB; HostDB:geneid_386575; -. DR eggNOG; KOG3070; Eukaryota. DR HOGENOM; CLU_063071_1_0_1; -. DR InParanoid; Q06066; -. DR Proteomes; UP000000539; Unassembled WGS sequence. 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:0005634; C:nucleus; IBA:GO_Central. DR GO; GO:0000932; C:P-body; IEA:UniProtKB-SubCell. DR GO; GO:0062153; F:C5-methylcytidine-containing RNA reader activity; ISS:UniProtKB. DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW. DR GO; GO:0035198; F:miRNA binding; ISS:UniProtKB. DR GO; GO:0003676; F:nucleic acid binding; IBA:GO_Central. DR GO; GO:0003723; F:RNA binding; ISS:UniProtKB. DR GO; GO:0048598; P:embryonic morphogenesis; ISS:UniProtKB. DR GO; GO:0008544; P:epidermis development; ISS:UniProtKB. 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:2000773; P:negative regulation of cellular senescence; ISS:UniProtKB. DR GO; GO:0017148; P:negative regulation of translation; ISS:UniProtKB. DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central. 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; Nucleic acid-binding proteins; 1. DR InterPro; IPR011129; CSD. DR InterPro; IPR019844; CSD_1. DR InterPro; IPR002059; CSP_DNA-bd. DR InterPro; IPR012340; NA-bd_OB-fold. DR PANTHER; PTHR11544; COLD SHOCK DOMAIN CONTAINING PROTEINS; 1. DR PANTHER; PTHR11544:SF68; Y-BOX-BINDING PROTEIN 1; 1. DR Pfam; PF00313; CSD; 1. DR PRINTS; PR00050; COLDSHOCK. DR SMART; SM00357; CSP; 1. DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1. DR PROSITE; PS00352; CSD_1; 1. DR PROSITE; PS51857; CSD_2; 1. PE 2: Evidence at transcript level; KW Cytoplasm; DNA-binding; mRNA processing; mRNA splicing; Nucleus; KW Reference proteome; Repressor; RNA-binding; Secreted; Transcription; KW Transcription regulation. FT CHAIN 1..321 FT /note="Y-box-binding protein 1" FT /id="PRO_0000100222" FT DOMAIN 58..122 FT /note="CSD" FT REGION 1..47 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 15..68 FT /note="Interaction with ss-DNA" FT /evidence="ECO:0000250" FT REGION 62..67 FT /note="C5-methylcytosine binding" FT /evidence="ECO:0000250|UniProtKB:P67809" FT REGION 117..321 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 153..168 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 247..266 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 285..303 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT SITE 62 FT /note="Important for C5-methylcytosine-recognition" FT /evidence="ECO:0000250|UniProtKB:P67809" SQ SEQUENCE 321 AA; 35799 MW; 6496F306C1432274 CRC64; MSSEAETQPP AAPVPAAPAA APADSKPNGG SGNGSSGLAS AAPPAGGDKK VIATKVLGTV KWFNVRNGYG FINRNDTKED VFVHQTAIKK NNPRKYLRSV GDGETVEFDV VEGEKGAEAA NVTGPGGVPV QGSKYAADRN HYRRYPRRRG PPRNYQQNYQ NSESGEKNEG AENIPEGQAQ QRRPYRRRRY PPYYMRRPYG RRPQYSNPPV QGEIVEGADN QGAGEQGRPV RQNMYRGYRP RFRRGPPRQR QPREDGNEED KENQGDETQG QQPPQRRYRR NFNYRRRRPE NPKPQDGKET KTAEPPAENT SAPEAEQGGA E //