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Q96DI7 (SNR40_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 126. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
U5 small nuclear ribonucleoprotein 40 kDa protein

Short name=U5 snRNP 40 kDa protein
Short name=U5-40K
Alternative name(s):
38 kDa-splicing factor
Prp8-binding protein
Short name=hPRP8BP
U5 snRNP-specific 40 kDa protein
WD repeat-containing protein 57
Gene names
Name:SNRNP40
Synonyms:PRP8BP, SFP38, WDR57
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length357 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Component of the U5 small nuclear ribonucleoprotein (snRNP) complex. The U5 snRNP is part of the spliceosome, a multiprotein complex that catalyzes the removal of introns from pre-messenger RNAs. Ref.1

Subunit structure

Identified in the spliceosome C complex. Part of the U5 snRNP complex. Interacts with PRPF8. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, NHP2L1, EFTUD2, SART1 and USP39. Ref.1 Ref.4 Ref.5 Ref.6

Subcellular location

Nucleus Ref.4.

Sequence similarities

Contains 7 WD repeats.

Sequence caution

The sequence AAC64084.1 differs from that shown. Reason: Frameshift at position 319. An insertion/deletion of a short nucleotide stretch in its cDNA resulting in a frameshift.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

PRPF8Q6P2Q93EBI-538492,EBI-538479

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 357357U5 small nuclear ribonucleoprotein 40 kDa protein
PRO_0000051417

Regions

Repeat64 – 10340WD 1
Repeat107 – 14640WD 2
Repeat149 – 18941WD 3
Repeat191 – 23040WD 4
Repeat233 – 27240WD 5
Repeat283 – 32240WD 6
Repeat325 – 35733WD 7

Experimental info

Sequence conflict31E → D in AAC69625. Ref.1
Sequence conflict162 – 1632RG → KS in AAC69625. Ref.1
Sequence conflict1871I → V in AAC64084. Ref.4
Sequence conflict3431I → L Ref.4

Sequences

Sequence LengthMass (Da)Tools
Q96DI7 [UniParc].

Last modified December 1, 2001. Version 1.
Checksum: DE8CADEB098E560C

FASTA35739,311
        10         20         30         40         50         60 
MIEQQKRKGP ELPLVPVKRQ RHELLLGAGS GPGAGQQQAT PGALLQAGPP RCSSLQAPIM 

        70         80         90        100        110        120 
LLSGHEGEVY CCKFHPNGST LASAGFDRLI LLWNVYGDCD NYATLKGHSG AVMELHYNTD 

       130        140        150        160        170        180 
GSMLFSASTD KTVAVWDSET GERVKRLKGH TSFVNSCYPA RRGPQLVCTG SDDGTVKLWD 

       190        200        210        220        230        240 
IRKKAAIQTF QNTYQVLAVT FNDTSDQIIS GGIDNDIKVW DLRQNKLTYT MRGHADSVTG 

       250        260        270        280        290        300 
LSLSSEGSYL LSNAMDNTVR VWDVRPFAPK ERCVKIFQGN VHNFEKNLLR CSWSPDGSKI 

       310        320        330        340        350 
AAGSADRFVY VWDTTSRRIL YKLPGHAGSI NEVAFHPDEP IIISASSDKR LYMGEIQ 

« Hide

References

« Hide 'large scale' references
[1]"The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an RNA unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein."
Achsel T., Ahrens K., Brahms H., Teigelkamp S., Luehrmann R.
Mol. Cell. Biol. 18:6756-6766(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, IDENTIFICATION IN U5 SNRP COMPLEX, INTERACTION WITH PRPF8.
[2]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"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].
Tissue: Placenta.
[4]"Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex."
Neubauer G., King A., Rappsilber J., Calvio C., Watson M., Ajuh P., Sleeman J., Lamond A.I., Mann M.
Nat. Genet. 20:46-50(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 60-357, IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, IDENTIFICATION IN SPLICEOSOMAL COMPLEX.
[5]"Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis."
Jurica M.S., Licklider L.J., Gygi S.P., Grigorieff N., Moore M.J.
RNA 8:426-439(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOME C COMPLEX.
[6]"The network of protein-protein interactions within the human U4/U6.U5 tri-snRNP."
Liu S., Rauhut R., Vornlocher H.-P., Luehrmann R.
RNA 12:1418-1430(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT.
[7]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[8]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF090988 mRNA. Translation: AAC69625.1.
AL451070, AC114495 Genomic DNA. Translation: CAH71848.1.
BC001494 mRNA. Translation: AAH01494.1.
AF083383 mRNA. Translation: AAC64084.1. Sequence problems.
CCDSCCDS340.1.
RefSeqNP_004805.2. NM_004814.2.
UniGeneHs.33962.

3D structure databases

ProteinModelPortalQ96DI7.
SMRQ96DI7. Positions 9-349.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114805. 39 interactions.
IntActQ96DI7. 21 interactions.
MINTMINT-1410013.
STRING9606.ENSP00000263694.

PTM databases

PhosphoSiteQ96DI7.

Polymorphism databases

DMDM67462075.

Proteomic databases

MaxQBQ96DI7.
PaxDbQ96DI7.
PeptideAtlasQ96DI7.
PRIDEQ96DI7.

Protocols and materials databases

DNASU9410.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000263694; ENSP00000263694; ENSG00000060688.
GeneID9410.
KEGGhsa:9410.
UCSCuc001bso.3. human.

Organism-specific databases

CTD9410.
GeneCardsGC01M031732.
HGNCHGNC:30857. SNRNP40.
HPAHPA026527.
HPA027345.
MIM607797. gene.
neXtProtNX_Q96DI7.
PharmGKBPA164726132.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG2319.
HOGENOMHOG000091644.
HOVERGENHBG105197.
InParanoidQ96DI7.
KOK12857.
OrthoDBEOG7992QT.
PhylomeDBQ96DI7.
TreeFamTF300039.

Enzyme and pathway databases

ReactomeREACT_71. Gene Expression.
SignaLinkQ96DI7.

Gene expression databases

ArrayExpressQ96DI7.
BgeeQ96DI7.
CleanExHS_SNRNP40.
GenevestigatorQ96DI7.

Family and domain databases

Gene3D2.130.10.10. 1 hit.
InterProIPR020472. G-protein_beta_WD-40_rep.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]
PfamPF00400. WD40. 7 hits.
[Graphical view]
PRINTSPR00320. GPROTEINBRPT.
SMARTSM00320. WD40. 7 hits.
[Graphical view]
SUPFAMSSF50978. SSF50978. 1 hit.
PROSITEPS00678. WD_REPEATS_1. 5 hits.
PS50082. WD_REPEATS_2. 7 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSNRNP40. human.
GeneWikiWDR57.
GenomeRNAi9410.
NextBio35252.
PROQ96DI7.
SOURCESearch...

Entry information

Entry nameSNR40_HUMAN
AccessionPrimary (citable) accession number: Q96DI7
Secondary accession number(s): O75938, O95320
Entry history
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: December 1, 2001
Last modified: July 9, 2014
This is version 126 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 1

Human chromosome 1: entries, gene names and cross-references to MIM