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Protein

WW domain-binding protein 4

Gene

WBP4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Promotes pre-mRNA splicing. A spliceosome-associated protein; may play a role in cross-intron bridging of U1 and U2 snRNPs in the mammalian A complex.2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri11 – 4232Matrin-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • nucleic acid binding Source: InterPro
  • proline-rich region binding Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

  • mRNA cis splicing, via spliceosome Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

SignaLinkiO75554.

Names & Taxonomyi

Protein namesi
Recommended name:
WW domain-binding protein 4
Short name:
WBP-4
Alternative name(s):
Formin-binding protein 21
WW domain-containing-binding protein 4
Gene namesi
Name:WBP4
Synonyms:FBP21, FNBP21
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 13

Organism-specific databases

HGNCiHGNC:12739. WBP4.

Subcellular locationi

GO - Cellular componenti

  • nuclear speck Source: UniProtKB
  • nucleoplasm Source: HPA
  • plasma membrane Source: HPA
  • spliceosomal complex Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi150 – 1501W → A: Nearly abolishes activation of pre-mRNA splicing. Abolishes interaction with WBP11. 1 Publication
Mutagenesisi191 – 1911W → A: Nearly abolishes activation of pre-mRNA splicing. Abolishes interaction with WBP11. 1 Publication

Organism-specific databases

PharmGKBiPA37350.

Polymorphism and mutation databases

BioMutaiWBP4.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 376376WW domain-binding protein 4PRO_0000076065Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei220 – 2201Phosphoserine2 Publications
Modified residuei262 – 2621Phosphoserine2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiO75554.
PaxDbiO75554.
PRIDEiO75554.

PTM databases

PhosphoSiteiO75554.

Expressioni

Gene expression databases

BgeeiO75554.
CleanExiHS_WBP4.
GenevisibleiO75554. HS.

Organism-specific databases

HPAiHPA038965.

Interactioni

Subunit structurei

Associated with U2 snRNPs. Binds splicing factors SNRPB, SNRPC and SF1. Interacts via the WW domains with the Pro-rich domains of KHDRBS1/SAM68 (By similarity). Interacts via the WW domains with the Pro-rich domains of WBP11.By similarity2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
HTTP428583EBI-7251981,EBI-466029

Protein-protein interaction databases

BioGridi116363. 45 interactions.
IntActiO75554. 2 interactions.
MINTiMINT-127038.
STRINGi9606.ENSP00000368801.

Structurei

Secondary structure

1
376
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi128 – 1303Combined sources
Turni134 – 1363Combined sources
Beta strandi140 – 1456Combined sources
Beta strandi148 – 1514Combined sources
Beta strandi161 – 1644Combined sources
Beta strandi168 – 1747Combined sources
Turni175 – 1773Combined sources
Beta strandi178 – 1836Combined sources
Turni184 – 1874Combined sources
Beta strandi188 – 1925Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DK1NMR-A127-163[»]
2JXWNMR-A122-196[»]
ProteinModelPortaliO75554.
SMRiO75554. Positions 122-196.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO75554.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini122 – 15534WW 1PROSITE-ProRule annotationAdd
BLAST
Domaini163 – 19634WW 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi111 – 12515Lys-richAdd
BLAST

Domaini

The WW domain recognizes the proline, glycine and methionine-rich (PGM) motif present in the splicing factors, as well as the Arg/Gly-rich-flanked Pro-rich domains found in several WW domain-binding proteins.By similarity

Sequence similaritiesi

Contains 1 matrin-type zinc finger.PROSITE-ProRule annotation
Contains 2 WW domains.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri11 – 4232Matrin-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG5104.
GeneTreeiENSGT00390000013956.
HOGENOMiHOG000067962.
HOVERGENiHBG053152.
InParanoidiO75554.
KOiK13220.
OMAiESHEEVD.
OrthoDBiEOG7H7930.
PhylomeDBiO75554.
TreeFamiTF316671.

Family and domain databases

InterProiIPR001202. WW_dom.
IPR000690. Znf_C2H2_matrin.
IPR003604. Znf_U1.
IPR013085. Znf_U1-C.
[Graphical view]
PfamiPF00397. WW. 2 hits.
PF06220. zf-U1. 1 hit.
[Graphical view]
SMARTiSM00456. WW. 2 hits.
SM00451. ZnF_U1. 1 hit.
[Graphical view]
SUPFAMiSSF51045. SSF51045. 2 hits.
PROSITEiPS01159. WW_DOMAIN_1. 2 hits.
PS50020. WW_DOMAIN_2. 2 hits.
PS50171. ZF_MATRIN. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O75554-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MADYWKSQPK KFCDYCKCWI ADNRPSVEFH ERGKNHKENV AKRISEIKQK
60 70 80 90 100
SLDKAKEEEK ASKEFAAMEA AALKAYQEDL KRLGLESEIL EPSITPVTST
110 120 130 140 150
IPPTSTSNQQ KEKKEKKKRK KDPSKGRWVE GITSEGYHYY YDLISGASQW
160 170 180 190 200
EKPEGFQGDL KKTAVKTVWV EGLSEDGFTY YYNTETGESR WEKPDDFIPH
210 220 230 240 250
TSDLPSSKVN ENSLGTLDES KSSDSHSDSD GEQEAEEGGV STETEKPKIK
260 270 280 290 300
FKEKNKNSDG GSDPETQKEK SIQKQNSLGS NEEKSKTLKK SNPYGEWQEI
310 320 330 340 350
KQEVESHEEV DLELPSTENE YVSTSEADGG GEPKVVFKEK TVTSLGVMAD
360 370
GVAPVFKKRR TENGKSRNLR QRGDDQ
Length:376
Mass (Da):42,507
Last modified:November 1, 1998 - v1
Checksum:i7A122A29D4325D11
GO
Isoform 2 (identifier: O75554-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     26-46: Missing.

Note: No experimental confirmation available.
Show »
Length:355
Mass (Da):40,030
Checksum:iCB1274E9A8A9BE99
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti113 – 1131K → R in a breast cancer sample; somatic mutation. 1 Publication
VAR_036352

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei26 – 4621Missing in isoform 2. 1 PublicationVSP_056413Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF071185 mRNA. Translation: AAC34811.1.
AK297536 mRNA. Translation: BAH12608.1.
AL157877 Genomic DNA. Translation: CAI13223.1.
BC104879 mRNA. Translation: AAI04880.1.
BC108310 mRNA. Translation: AAI08311.1.
CCDSiCCDS9375.1. [O75554-1]
RefSeqiNP_009118.1. NM_007187.3. [O75554-1]
UniGeneiHs.411300.

Genome annotation databases

EnsembliENST00000379487; ENSP00000368801; ENSG00000120688. [O75554-1]
GeneIDi11193.
KEGGihsa:11193.
UCSCiuc001uxt.3. human. [O75554-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF071185 mRNA. Translation: AAC34811.1.
AK297536 mRNA. Translation: BAH12608.1.
AL157877 Genomic DNA. Translation: CAI13223.1.
BC104879 mRNA. Translation: AAI04880.1.
BC108310 mRNA. Translation: AAI08311.1.
CCDSiCCDS9375.1. [O75554-1]
RefSeqiNP_009118.1. NM_007187.3. [O75554-1]
UniGeneiHs.411300.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2DK1NMR-A127-163[»]
2JXWNMR-A122-196[»]
ProteinModelPortaliO75554.
SMRiO75554. Positions 122-196.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116363. 45 interactions.
IntActiO75554. 2 interactions.
MINTiMINT-127038.
STRINGi9606.ENSP00000368801.

PTM databases

PhosphoSiteiO75554.

Polymorphism and mutation databases

BioMutaiWBP4.

Proteomic databases

MaxQBiO75554.
PaxDbiO75554.
PRIDEiO75554.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000379487; ENSP00000368801; ENSG00000120688. [O75554-1]
GeneIDi11193.
KEGGihsa:11193.
UCSCiuc001uxt.3. human. [O75554-1]

Organism-specific databases

CTDi11193.
GeneCardsiGC13P041635.
HGNCiHGNC:12739. WBP4.
HPAiHPA038965.
MIMi604981. gene.
neXtProtiNX_O75554.
PharmGKBiPA37350.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG5104.
GeneTreeiENSGT00390000013956.
HOGENOMiHOG000067962.
HOVERGENiHBG053152.
InParanoidiO75554.
KOiK13220.
OMAiESHEEVD.
OrthoDBiEOG7H7930.
PhylomeDBiO75554.
TreeFamiTF316671.

Enzyme and pathway databases

SignaLinkiO75554.

Miscellaneous databases

EvolutionaryTraceiO75554.
GeneWikiiWBP4.
GenomeRNAii11193.
NextBioi35479506.
PROiO75554.
SOURCEiSearch...

Gene expression databases

BgeeiO75554.
CleanExiHS_WBP4.
GenevisibleiO75554. HS.

Family and domain databases

InterProiIPR001202. WW_dom.
IPR000690. Znf_C2H2_matrin.
IPR003604. Znf_U1.
IPR013085. Znf_U1-C.
[Graphical view]
PfamiPF00397. WW. 2 hits.
PF06220. zf-U1. 1 hit.
[Graphical view]
SMARTiSM00456. WW. 2 hits.
SM00451. ZnF_U1. 1 hit.
[Graphical view]
SUPFAMiSSF51045. SSF51045. 2 hits.
PROSITEiPS01159. WW_DOMAIN_1. 2 hits.
PS50020. WW_DOMAIN_2. 2 hits.
PS50171. ZF_MATRIN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "WW domain-mediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif."
    Bedford M.T., Reed R., Leder P.
    Proc. Natl. Acad. Sci. U.S.A. 95:10602-10607(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH SNRPB; SNRPC; SF1 AND U2.
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Brain.
  3. "The DNA sequence and analysis of human chromosome 13."
    Dunham A., Matthews L.H., Burton J., Ashurst J.L., Howe K.L., Ashcroft K.J., Beare D.M., Burford D.C., Hunt S.E., Griffiths-Jones S., Jones M.C., Keenan S.J., Oliver K., Scott C.E., Ainscough R., Almeida J.P., Ambrose K.D., Andrews D.T.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Bannerjee R., Barlow K.F., Bates K., Beasley H., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burrill W., Carder C., Carter N.P., Chapman J.C., Clamp M.E., Clark S.Y., Clarke G., Clee C.M., Clegg S.C., Cobley V., Collins J.E., Corby N., Coville G.J., Deloukas P., Dhami P., Dunham I., Dunn M., Earthrowl M.E., Ellington A.G., Faulkner L., Frankish A.G., Frankland J., French L., Garner P., Garnett J., Gilbert J.G.R., Gilson C.J., Ghori J., Grafham D.V., Gribble S.M., Griffiths C., Hall R.E., Hammond S., Harley J.L., Hart E.A., Heath P.D., Howden P.J., Huckle E.J., Hunt P.J., Hunt A.R., Johnson C., Johnson D., Kay M., Kimberley A.M., King A., Laird G.K., Langford C.J., Lawlor S., Leongamornlert D.A., Lloyd D.M., Lloyd C., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., McLaren S.J., McMurray A., Milne S., Moore M.J.F., Nickerson T., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K.M., Rice C.M., Searle S., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Steward C.A., Sycamore N., Tester J., Thomas D.W., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Wilming L., Wray P.W., Wright M.W., Young L., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Beck S., Bentley D.R., Rogers J., Ross M.T.
    Nature 428:522-528(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  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] (ISOFORM 1).
    Tissue: Brain and Testis.
  5. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
    Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
    Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-220, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  6. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-220 AND SER-262, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-262, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  8. "Solution structure of WW domain in WW domain binding protein 4 (WBP-4)."
    RIKEN structural genomics initiative (RSGI)
    Submitted (OCT-2006) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 124-164.
  9. "Structure and function of the two tandem WW domains of the pre-mRNA splicing factor FBP21 (formin-binding protein 21)."
    Huang X., Beullens M., Zhang J., Zhou Y., Nicolaescu E., Lesage B., Hu Q., Wu J., Bollen M., Shi Y.
    J. Biol. Chem. 284:25375-25387(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 122-196, FUNCTION, MUTAGENESIS OF TRP-150 AND TRP-191, SUBCELLULAR LOCATION, INTERACTION WITH WBP11.
  10. Cited for: VARIANT [LARGE SCALE ANALYSIS] ARG-113.

Entry informationi

Entry nameiWBP4_HUMAN
AccessioniPrimary (citable) accession number: O75554
Secondary accession number(s): B7Z4M2, Q32P29
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: November 1, 1998
Last modified: June 24, 2015
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 13
    Human chromosome 13: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.