Reviewed, UniProtKB/Swiss-Prot P67809 (YBOX1_HUMAN)

Names and origin

Protein names

Recommended name:
    Nuclease-sensitive element-binding protein 1
Alternative name(s):
    Y-box-binding protein 1
    Y-box transcription factor
    YB-1
    CCAAT-binding transcription factor I subunit A
      Short name=CBF-A
    Enhancer factor I subunit A
      Short name=EFI-A
    DNA-binding protein B
      Short name=DBPB

Gene names

Name:	YBX1
Synonyms:	NSEP1, YB1

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	324 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	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. 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.
Subunit structure	Component of cytoplasmic messenger ribonucleoprotein particles (mRNPs). Interacts with AKT1, SFRS9, THOC4, MSH2, XRCC5, 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. Ref.6 Ref.8 Ref.9 Ref.10 Ref.11 Ref.19
Subcellular location	Cytoplasm. Nucleus. Note: Shuttles between nucleus and cytoplasm. Predominantly cytoplasmic in proliferating cells. Cytotoxic stress and DNA damage enhance translocation to the nucleus. Ref.8 Ref.10 Ref.11
Post-translational modification	In the absence of phosphorylation the protein is retained in the cytoplasm. 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.
Sequence caution	The sequence AAA59949.1 differs from that shown. Reason: Frameshift at several positions.

Ontologies

Keywords
Biological process	Transcription Transcription regulation mRNA processing mRNA splicing
Cellular component	Cytoplasm Nucleus
Ligand	DNA-binding RNA-binding
Molecular function	Repressor
PTM	Isopeptide bond Phosphoprotein Ubl conjugation
Technical term	3D-structure
Gene Ontology (GO)
Biological process	nuclear mRNA splicing, via spliceosome Inferred from Experiment. Source: Reactome regulation of transcription, DNA-dependent Non-traceable author statement. Source: UniProtKB transcription from RNA polymerase II promoter Ref.2 Traceable author statement. Source: ProtInc
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Ref.2 Non-traceable author statement. Source: UniProtKB
Molecular function	RNA binding Non-traceable author statement. Source: UniProtKB double-stranded DNA binding Traceable author statement. Source: ProtInc protein binding Inferred from physical interaction. Source: IntAct single-stranded DNA binding Traceable author statement. Source: ProtInc transcription factor activity Ref.2 Traceable author statement. Source: ProtInc transcription repressor activity Non-traceable author statement. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CTCF	Q08705	2	EBI-354065,EBI-932806	From a different organism.
HNRNPD	Q14103-3	2	EBI-354065,EBI-432539
HNRNPD	Q14103-4	3	EBI-354065,EBI-432545

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed

Chain

2 – 324

323

Nuclease-sensitive element-binding protein 1

PRO_0000100219

Regions

Domain

61 – 125

65

CSD

Region

15 – 71

57

Interaction with ss-DNA

Sites

Site

219 – 220

2

Cleavage; by 20S proteasomal protease

Amino acid modifications

Modified residue

102

1

Phosphoserine; by PKB/AKT1 Ref.11

Modified residue

162

1

Phosphotyrosine Ref.12

Modified residue

165

1

Phosphoserine Ref.14 Ref.17

Modified residue

167

1

Phosphoserine Ref.14

Modified residue

174

1

Phosphoserine Ref.14 Ref.17 Ref.13

Modified residue

176

1

Phosphoserine Ref.17 Ref.13

Modified residue

314

1

Phosphoserine Ref.13 Ref.15

Cross-link

137

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.16

Experimental info

Mutagenesis

102

1

S → A: Loss of phosphorylation by PKB/AKT1. Inhibits translocation to the nucleus and tumor cell growth. Ref.11

Sequence conflict

120

1

A → E in AAA61308. Ref.2

Sequence conflict

314 – 324

11

SAPEAEQGGAE → RSR Ref.2

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

324

Helix Strand Turn

Details...

Beta strand

56 – 67

12

Turn

68 – 71

4

Beta strand

72 – 77

6

Turn

78 – 81

4

Beta strand

82 – 87

6

Helix

88 – 90

3

Beta strand

108 – 115

8

Beta strand

117 – 125

9

Sequences

	Sequence		Length	Mass (Da)
	P67809-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: DF0114BF974AEDB8	FASTA	324	35,924
	10 20 30 40 50 60 MSSEAETQQP PAAPPAAPAL SAADTKPGTT GSGAGSGGPG GLTSAAPAGG DKKVIATKVL 70 80 90 100 110 120 GTVKWFNVRN GYGFINRNDT KEDVFVHQTA IKKNNPRKYL RSVGDGETVE FDVVEGEKGA 130 140 150 160 170 180 EAANVTGPGG VPVQGSKYAA DRNHYRRYPR RRGPPRNYQQ NYQNSESGEK NEGSESAPEG 190 200 210 220 230 240 QAQQRRPYRR RRFPPYYMRR PYGRRPQYSN PPVQGEVMEG ADNQGAGEQG RPVRQNMYRG 250 260 270 280 290 300 YRPRFRRGPP RQRQPREDGN EEDKENQGDE TQGQQPPQRR YRRNFNYRRR RPENPKPQDG 310 320 KETKAADPPA ENSSAPEAEQ GGAE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Two human genes isolated by a novel method encode DNA-binding proteins containing a common region of homology." Sakura H., Maekawa T., Imamoto F., Yasuda K., Ishii S. Gene 73:499-507(1988) [PubMed: 2977358] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box." Didier D.K., Schiffenbauer J., Woulfe S.L., Zacheis M., Schwartz B.D. Proc. Natl. Acad. Sci. U.S.A. 85:7322-7326(1988) [PubMed: 3174636] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]	"Full length cDNA sequence encoding a nuclease-sensitive element DNA binding protein." Kolluri R., Kinniburgh A.J. Nucleic Acids Res. 19:4771-4771(1991) [PubMed: 1891370] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[4]	"A human protein containing a 'cold shock' domain binds specifically to H-DNA upstream from the human gamma-globin genes." Horwitz E.M., Maloney K.A., Ley T.J. J. Biol. Chem. 269:14130-14139(1994) [PubMed: 8188694] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Tissue: Bone marrow.
[5]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Adrenal cortex, Eye, Kidney, Muscle, Placenta, Skin, Testis and Uterus.
[6]	"Nucleolin and YB-1 are required for JNK-mediated interleukin-2 mRNA stabilization during T-cell activation." Chen C.-Y., Gherzi R., Andersen J.S., Gaietta G., Juerchott K., Royer H.-D., Mann M., Karin M. Genes Dev. 14:1236-1248(2000) [PubMed: 10817758] [Abstract] Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT.
[7]	"Y box-binding factor promotes eosinophil survival by stabilizing granulocyte-macrophage colony-stimulating factor mRNA." Capowski E.E., Esnault S., Bhattacharya S., Malter J.S. J. Immunol. 167:5970-5976(2001) [PubMed: 11698476] [Abstract] Cited for: FUNCTION.
[8]	"Splicing factor SRp30c interaction with Y-box protein-1 confers nuclear YB-1 shuttling and alternative splice site selection." Raffetseder U., Frye B., Rauen T., Juerchott K., Royer H.-D., Jansen P.L., Mertens P.R. J. Biol. Chem. 278:18241-18248(2003) [PubMed: 12604611] [Abstract] Cited for: FUNCTION, INTERACTION WITH SFRS9, SUBCELLULAR LOCATION.
[9]	"Regulation of alternative splicing by SRrp86 and its interacting proteins." Li J., Hawkins I.C., Harvey C.D., Jennings J.L., Link A.J., Patton J.G. Mol. Cell. Biol. 23:7437-7447(2003) [PubMed: 14559993] [Abstract] Cited for: INTERACTION WITH SFRS12.
[10]	"YB-1 promotes strand separation in vitro of duplex DNA containing either mispaired bases or cisplatin modifications, exhibits endonucleolytic activities and binds several DNA repair proteins." Gaudreault I., Guay D., Lebel M. Nucleic Acids Res. 32:316-327(2004) [PubMed: 14718551] [Abstract] Cited for: FUNCTION, SUBUNIT, SUBCELLULAR LOCATION, INTERACTION WITH THOC4; NCL; XRCC5; WRN AND MSH2.
[11]	"Akt phosphorylates the Y-box binding protein 1 at Ser102 located in the cold shock domain and affects the anchorage-independent growth of breast cancer cells." Sutherland B.W., Kucab J., Wu J., Lee C., Cheang M.C.U., Yorida E., Turbin D., Dedhar S., Nelson C., Pollak M., Leighton Grimes H., Miller K., Badve S., Huntsman D., Blake-Gilks C., Chen M., Pallen C.J., Dunn S.E. Oncogene 24:4281-4292(2005) [PubMed: 15806160] [Abstract] Cited for: PHOSPHORYLATION AT SER-102, INTERACTION WITH AKT1, SUBCELLULAR LOCATION, MUTAGENESIS OF SER-102.
[12]	"Immunoaffinity profiling of tyrosine phosphorylation in cancer cells." Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.-M., Polakiewicz R.D., Comb M.J. Nat. Biotechnol. 23:94-101(2005) [PubMed: 15592455] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-162, MASS SPECTROMETRY.
[13]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed: 17081983] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174; SER-176 AND SER-314, MASS SPECTROMETRY. Tissue: Epithelium.
[14]	"Toward a global characterization of the phosphoproteome in prostate cancer cells: identification of phosphoproteins in the LNCaP cell line." Giorgianni F., Zhao Y., Desiderio D.M., Beranova-Giorgianni S. Electrophoresis 28:2027-2034(2007) [PubMed: 17487921] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-165; SER-167 AND SER-174, MASS SPECTROMETRY.
[15]	"Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry." Molina H., Horn D.M., Tang N., Mathivanan S., Pandey A. Proc. Natl. Acad. Sci. U.S.A. 104:2199-2204(2007) [PubMed: 17287340] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-314, MASS SPECTROMETRY.
[16]	"Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry." Meierhofer D., Wang X., Huang L., Kaiser P. J. Proteome Res. 7:4566-4576(2008) [PubMed: 18781797] [Abstract] Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-137, MASS SPECTROMETRY.
[17]	"A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-165; SER-174 AND SER-176, MASS SPECTROMETRY.
[18]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[19]	"The solution structure and DNA-binding properties of the cold-shock domain of the human Y-box protein YB-1." Kloks C.P.A.M., Spronk C.A.E.M., Lasonder E., Hoffmann A., Vuister G.W., Grzesiek S., Hilbers C.W. J. Mol. Biol. 316:317-326(2002) [PubMed: 11851341] [Abstract] Cited for: STRUCTURE BY NMR OF 52-129, INTERACTION WITH SS-DNA.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M24070 mRNA. Translation: AAA35750.1. Different initiation.
J03827 mRNA. Translation: AAA61308.1.
M83234 mRNA. Translation: AAA59949.1. Frameshift.
L28809 mRNA. Translation: AAA20871.1.
BC002411 mRNA. Translation: AAH02411.1.
BC010430 mRNA. Translation: AAH10430.1.
BC015208 mRNA. Translation: AAH15208.1.
BC038384 mRNA. Translation: AAH38384.1.
BC065571 mRNA. Translation: AAH65571.1.
BC070084 mRNA. Translation: AAH70084.1.
BC071708 mRNA. Translation: AAH71708.1.
BC090038 mRNA. Translation: AAH90038.1.
BC098435 mRNA. Translation: AAH98435.1.
BC106045 mRNA. Translation: AAI06046.1.

IPI

IPI00031812.

PIR

I39382.
S34426.

RefSeq

NP_004550.2.

UniGene

Hs.473583

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1H95	NMR	-	A	52-129	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P67809. 13 interactions.

PTM databases

PhosphoSite

P67809.

Proteomic databases

PRIDE

P67809.

Genome annotation databases

Ensembl

ENSG00000065978. Homo sapiens. [Contig view]

GeneID

4904.

KEGG

hsa:4904.

Organism-specific databases

GeneCards

GC01P042920.

H-InvDB

HIX0000491.

HGNC

HGNC:8014. YBX1.

HPA

CAB005875.

MIM

154030. gene.

PharmGKB

PA31791.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

P67809.

HOVERGEN

P67809.

OMA

P67809. PAENTSA.

Enzyme and pathway databases

Pathway_Interaction_DB

ptp1bpathway. Signaling events mediated by PTP1B.

Reactome

REACT_1675. mRNA Processing.
REACT_6167. Influenza Infection.
REACT_71. Gene Expression.

Gene expression databases

CleanEx

HS_YBX1.

GermOnline

ENSG00000065978. Homo sapiens.

Family and domain databases

InterPro

IPR019844. Cold-shock_conserved_site.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA_bd.
IPR012340. NA-bd_OB-fold.
[Graphical view]

Gene3D

G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.

Pfam

PF00313. CSD. 1 hit.
[Graphical view]

PRINTS

PR00050. COLDSHOCK.

ProDom

PD000621. Cold_shock. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00357. CSP. 1 hit.
[Graphical view]

PROSITE

PS00352. COLD_SHOCK. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

18871.

PMAP-CutDB

P67809.

SOURCE

Search...

Entry information

Entry name

YBOX1_HUMAN

Accession

Primary (citable) accession number: P67809
Secondary accession number(s): P16990 , P16991, Q14972, Q15325, Q5FVF0

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 11, 2004
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 64 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)