UniProt Accession

 YBOX1_HUMAN; P67809; P16990; P16991; Q14972; Q15325; Q5FVF0 

Genbank Protein ID

 M24070; J03827; M83234; L28809; BC002411; BC010430; BC015208; BC038384; BC065571; BC070084; BC071708; BC090038; BC098435; BC106045 

Genbank Nucleotide ID

 AAA35750.1; AAA61308.1; AAA59949.1; AAA20871.1; AAH02411.1; AAH10430.1; AAH15208.1; AAH38384.1; AAH65571.1; AAH70084.1; AAH71708.1; AAH90038.1; AAH98435.1; AAI06046.1 

Protein Name

 Nuclease-sensitive element-binding protein 1 

Protein Synonyms/Alias

 CCAAT-binding transcription factor I subunit A; CBF-A; DNA-binding protein B; DBPB; Enhancer factor I subunit A; EFI-A; Y-box transcription factor; Y-box-binding protein 1; YB-1 

Gene Name

 YBX1 

Gene Synonyms/Alias

 NSEP1; YB1 

Created Date

 July 27, 2013 

Organism

 Homo sapiens (Human) 

NCBI Taxa ID

 9606 

Lysine Modification

Position	Peptide	Type	References
26	ALSAADTKPGTTGSG	ubiquitination	[1, 2]
52	AAPAGGDKKVIATKV	ubiquitination	[2, 3]
53	APAGGDKKVIATKVL	ubiquitination	[2]
58	DKKVIATKVLGTVKW	ubiquitination	[3, 4]
64	TKVLGTVKWFNVRNG	ubiquitination	[1, 2, 3, 4, 5, 6]
81	FINRNDTKEDVFVHQ	ubiquitination	[1, 3, 5, 7]
92	FVHQTAIKKNNPRKY	methylation	[8]
92	FVHQTAIKKNNPRKY	ubiquitination	[1, 3, 4, 5, 7]
93	VHQTAIKKNNPRKYL	ubiquitination	[3, 5, 7]
118	FDVVEGEKGAEAANV	ubiquitination	[3, 5]
137	GVPVQGSKYAADRNH	ubiquitination	[1, 2, 3, 4, 5, 7, 9, 10, 11]
170	QNSESGEKNEGSESA	ubiquitination	[2, 3, 4, 5]
264	EDGNEEDKENQGDET	ubiquitination	[3, 5]
301	NPKPQDGKETKAADP	ubiquitination	[5]
304	PQDGKETKAADPPAE	ubiquitination	[3, 5]

Reference

 [1] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [2] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [3] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [4] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [5] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [6] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [7] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [8] Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome.
 Bremang M, Cuomo A, Agresta AM, Stugiewicz M, Spadotto V, Bonaldi T.
 Mol Biosyst. 2013 Jul 30;9(9):2231-47. [PMID: 23748837]
 [9] Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry.
 Meierhofer D, Wang X, Huang L, Kaiser P.
 J Proteome Res. 2008 Oct;7(10):4566-76. [PMID: 18781797]
 [10] Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
 Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.
 Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. [PMID: 21139048]
 [11] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473] 

Functional Description

 Mediates pre-mRNA alternative splicing regulation. 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 (By similarity). Regulates the transcription of numerous genes. 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 to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II 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. Component of the CRD-mediated complex that promotes MYC mRNA stability. Binds preferentially to the 5'-[CU]CUGCG-3' motif in vitro. 

Sequence Annotation

 DOMAIN 61 125 CSD.
 REGION 15 71 Interaction with ss-DNA.
 MOD_RES 2 2 N-acetylserine.
 MOD_RES 102 102 Phosphoserine; by PKB/AKT1.
 MOD_RES 162 162 Phosphotyrosine.
 MOD_RES 165 165 Phosphoserine.
 MOD_RES 167 167 Phosphoserine.
 MOD_RES 174 174 Phosphoserine.
 MOD_RES 176 176 Phosphoserine.
 MOD_RES 301 301 N6-acetyllysine.
 MOD_RES 304 304 N6-acetyllysine.
 MOD_RES 314 314 Phosphoserine.
 CROSSLNK 137 137 Glycyl lysine isopeptide (Lys-Gly)  

Keyword

 3D-structure; Acetylation; Activator; Complete proteome; Cytoplasm; Direct protein sequencing; DNA-binding; Isopeptide bond; Mitogen; mRNA processing; mRNA splicing; Nucleus; Phosphoprotein; Reference proteome; Repressor; RNA-binding; Secreted; Transcription; Transcription regulation; Ubl conjugation. 

Sequence Source

 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 

Protein Length

 324 AA 

Protein Sequence

Gene Ontology

 GO:0070937; C:CRD-mediated mRNA stability complex; IDA:UniProtKB.
 GO:0010494; C:cytoplasmic stress granule; IDA:UniProtKB.
 GO:0005576; C:extracellular region; IEA:UniProtKB-SubCell.
 GO:0071204; C:histone pre-mRNA 3'end processing complex; ISS:UniProtKB.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0005689; C:U12-type spliceosomal complex; IDA:UniProtKB.
 GO:0003690; F:double-stranded DNA binding; TAS:ProtInc.
 GO:0003723; F:RNA binding; IDA:UniProtKB.
 GO:0003700; F:sequence-specific DNA binding transcription factor activity; TAS:ProtInc.
 GO:0003697; F:single-stranded DNA binding; TAS:ProtInc.
 GO:0070934; P:CRD-mediated mRNA stabilization; IMP:UniProtKB.
 GO:0001701; P:in utero embryonic development; IEA:Compara.
 GO:0000398; P:mRNA splicing, via spliceosome; TAS:Reactome.
 GO:0051154; P:negative regulation of striated muscle cell differentiation; IEA:Compara.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IEA:Compara.
 GO:0045892; P:negative regulation of transcription, DNA-dependent; NAS:UniProtKB.
 GO:0051781; P:positive regulation of cell division; IEA:UniProtKB-KW.
 GO:0006366; P:transcription from RNA polymerase II promoter; TAS:ProtInc. 

Interpro

 IPR019844; Cold-shock_CS.
 IPR011129; Cold_shock_prot.
 IPR002059; CSP_DNA-bd.
 IPR012340; NA-bd_OB-fold. 

Pfam

 PF00313; CSD 

SMART

 SM00357; CSP 

PROSITE

 PS00352; COLD_SHOCK 

PRINTS

 PR00050; COLDSHOCK.