Reviewed, UniProtKB/Swiss-Prot Q96DI7 (SNR40_HUMAN)

Names and origin

Protein names

Recommended name:
    U5 small nuclear ribonucleoprotein 40 kDa protein
      Short name=U5 snRNP 40 kDa protein
      Short name=U5-40K
Alternative name(s):
    U5 snRNP-specific 40 kDa protein
    38 kDa-splicing factor
    WD repeat-containing protein 57
    Prp8-binding protein
      Short name=hPRP8BP

Gene names

Name:	SNRNP40
Synonyms:	PRP8BP, SFP38, WDR57

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	357 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Subunit structure	Identified in the spliceosome C complex, at least composed of AQR, ASCC3L1, C19orf29, CDC40, CDC5L, CRNKL1, DDX23, DDX41, DDX48, DDX5, DGCR14, DHX35, DHX38, DHX8, EFTUD2, FRG1, GPATC1, HNRPA1, HNRPA2B1, HNRPA3, HNRPC, HNRPF, HNRPH1, HNRPK, HNRPM, HNRPR, HNRPU, KIAA1160, KIAA1604, LSM2, LSM3, MAGOH, MORG1, PABPC1, PLRG1, PNN, PPIE, PPIL1, PPIL3, PPWD1, PRPF19, PRPF4B, PRPF6, PRPF8, RALY, RBM22, RBM8A, RBMX, SART1, SF3A1, SF3A2, SF3A3, SF3B1, SF3B2, SF3B3, SFRS1, SKIV2L2, SNRPA1, SNRPB, SNRPB2, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, SNW1, SRRM1, SRRM2, SYF2, SYNCRIP, TFIP11, THOC4, U2AF1, SNRNP40, XAB2 and ZCCHC8. Part of the U5 snRNP complex. Interacts with PRPF8. Ref.1
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.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Domain	Repeat WD repeat
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	RNA splicing, via transesterification reactions Ref.1 Traceable author statement. Source: UniProtKB mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	U5 snRNP Ref.1 Traceable author statement. Source: ProtInc small nucleolar ribonucleoprotein complex Ref.1 Non-traceable author statement. Source: UniProtKB spliceosomal complex Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	protein binding Ref.1 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CD2BP2	O95400	1	EBI-538492,EBI-768015
DDX23	Q9BUQ8	1	EBI-538492,EBI-540096
EFTUD2	Q15029	2	EBI-538492,EBI-357897
MAGEA6	P43360	1	EBI-538492,EBI-1045155
PFDN2	Q9UHV9	1	EBI-538492,EBI-359873
PRPF6	O94906	1	EBI-538492,EBI-536755
PRPF8	Q6P2Q9	3	EBI-538492,EBI-538479
SF3B1	O75533	1	EBI-538492,EBI-876542
SNRNP200	O75643	2	EBI-538492,EBI-1045395
SNRPB2	P08579	1	EBI-538492,EBI-1053651

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 357	357	U5 small nuclear ribonucleoprotein 40 kDa protein		PRO_0000051417
Regions
	Repeat	64 – 103	40	WD 1
	Repeat	107 – 146	40	WD 2
	Repeat	149 – 189	41	WD 3
	Repeat	191 – 230	40	WD 4
	Repeat	233 – 272	40	WD 5
	Repeat	283 – 322	40	WD 6
	Repeat	325 – 357	33	WD 7
Experimental info
	Sequence conflict	3	1	E → D in AAC69625. Ref.1
	Sequence conflict	162 – 163	2	RG → KS in AAC69625. Ref.1
	Sequence conflict	187	1	I → V in AAC64084. Ref.4
	Sequence conflict	343	1	I → L Ref.4

Sequences

	Sequence		Length	Mass (Da)
	Q96DI7-1 [UniParc]. Last modified December 1, 2001. Version 1. Checksum: DE8CADEB098E560C	FASTA	357	39,311
	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

References

	« Hide 'large scale' referencesShow '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: 9774689] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], 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. , 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: 16710414] [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: 15489334] [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: 9731529] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 60-357, IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, IDENTIFICATION IN SPLICEOSOME 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: 11991638] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN THE SPLICEOSOME C COMPLEX.
[6]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
+	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.
IPI	IPI00940685.
RefSeq	NP_004805.2.
UniGene	Hs.33962
3D structure databases
SMR	Q96DI7. Positions 10-271, 61-352.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q96DI7. 16 interactions.
STRING	Q96DI7.
PTM databases
PhosphoSite	Q96DI7.
Proteomic databases
PeptideAtlas	Q96DI7.
PRIDE	Q96DI7.
Genome annotation databases
Ensembl	ENST00000263694; ENSP00000263694; ENSG00000060688; Homo sapiens. [Genome view]
GeneID	9410.
KEGG	hsa:9410.
UCSC	uc001bso.1. human.
Organism-specific databases
CTD	9410.
GeneCards	GC01M031506.
H-InvDB	HIX0000351.
HGNC	HGNC:30857. SNRNP40.
HPA	HPA026527. HPA027345.
MIM	607797. gene.
PharmGKB	PA142670591.
GenAtlas	Search...
Phylogenomic databases
HOVERGEN	Q96DI7.
InParanoid	Q96DI7.
PhylomeDB	Q96DI7.
Enzyme and pathway databases
Reactome	REACT_125. Processing of Capped Intron-Containing Pre-mRNA. REACT_71. Gene Expression.
Gene expression databases
ArrayExpress	Q96DI7.
Bgee	Q96DI7.
CleanEx	HS_SNRNP40.
Genevestigator	Q96DI7.
GermOnline	ENSG00000060688. Homo sapiens.
Family and domain databases
InterPro	IPR020472. G-protein_beta_WD-40_rep_reg. IPR015943. WD40/YVTN_repeat-like_dom. IPR001680. WD40_repeat. IPR011046. WD40_repeat-like_dom. IPR019782. WD40_repeat_2. IPR019775. WD40_repeat_CS. IPR017986. WD40_repeat_dom. IPR019781. WD40_repeat_sg. [Graphical view]
Gene3D	G3DSA:2.130.10.10. WD40/YVTN_repeat-like. 1 hit.
Pfam	PF00400. WD40. 7 hits. [Graphical view]
PRINTS	PR00320. GPROTEINBRPT.
SMART	SM00320. WD40. 7 hits. [Graphical view]
PROSITE	PS00678. WD_REPEATS_1. 5 hits. PS50082. WD_REPEATS_2. 7 hits. PS50294. WD_REPEATS_REGION. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	35252.
SOURCE	Search...

Entry information

Entry name

SNR40_HUMAN

Accession

Primary (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:	February 9, 2010
This is version 83 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

Disclaimer

Any 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.