O43172 (PRP4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
U4/U6 small nuclear ribonucleoprotein Prp4

Alternative name(s):
PRP4 homolog
Short name=hPrp4
U4/U6 snRNP 60 kDa protein
WD splicing factor Prp4

Gene names

Name:	PRPF4
Synonyms:	PRP4

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Dipnotetrapodomorpha › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Boreoeutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	522 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.
Subunit structure	Interacts directly with PRPF18, PPIH and PRPF3. Part of a heteromeric complex containing PPIH, PRPF3 and PRPF4 that is stable in the absence of RNA. 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.2 Ref.3 Ref.7 Ref.8
Subcellular location	Nucleus speckle By similarity. Note: Colocalizes with spliceosomal snRNPs By similarity.
Sequence similarities	Contains 7 WD repeats.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus Spliceosome
Coding sequence diversity	Alternative splicing
Domain	Repeat WD repeat
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	RNA processing Traceable author statement Ref.3. Source: ProtInc RNA splicing Traceable author statement. Source: Reactome RNA splicing, via transesterification reactions Non-traceable author statement Ref.3. Source: UniProtKB gene expression Traceable author statement. Source: Reactome mRNA splicing, via spliceosome Inferred by curator PubMed 9570313. Source: BHF-UCL
Cellular_component	Cajal body Inferred from direct assay PubMed 15257298. Source: BHF-UCL U4/U6 snRNP Inferred from direct assay PubMed 9570313. Source: BHF-UCL nuclear speck Inferred from electronic annotation. Source: UniProtKB-SubCell nucleoplasm Traceable author statement. Source: Reactome nucleus Inferred from direct assay. Source: HPA spliceosomal complex Non-traceable author statement Ref.3. Source: UniProtKB
Molecular_function	protein binding Inferred from physical interaction PubMed 19615732PubMed 22365833. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
GPKOW	Q92917	2	EBI-718395,EBI-746309
PPIH	O43447	2	EBI-718395,EBI-1055615

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: O43172-1)

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.

Isoform 2 (identifier: O43172-2)

The sequence of this isoform differs from the canonical sequence as follows:
     10-10: Missing.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 522

522

U4/U6 small nuclear ribonucleoprotein Prp4

PRO_0000051149

Regions

Repeat

229 – 268

40

WD 1

Repeat

271 – 318

48

WD 2

Repeat

321 – 360

40

WD 3

Repeat

363 – 402

40

WD 4

Repeat

405 – 444

40

WD 5

Repeat

447 – 487

41

WD 6

Repeat

490 – 521

32

WD 7

Amino acid modifications

Modified residue

27

1

N6-acetyllysine Ref.9

Natural variations

Alternative sequence

10

1

Missing in isoform 2.

VSP_006785

Experimental info

Sequence conflict

78 – 103

26

HISER…INVST → ISASDRQKYWLSLREGSEPG RSMFPP in AAC02261. Ref.3

Sequence conflict

78

1

H → R in AAC51925. Ref.2

Sequence conflict

86

1

V → L in AAB87640. Ref.1

Sequence conflict

134

1

R → K in AAB87640. Ref.1

Sequence conflict

141

1

G → D in AAB87640. Ref.1

Sequence conflict

176

1

Missing in AAC02261. Ref.3

Sequence conflict

275 – 282

8

NVGAIVFH → KKEQLHSI in AAC02261. Ref.3

Sequence conflict

405

1

G → D in AAB87640. Ref.1

Sequence conflict

447

1

A → P in AAB87640. Ref.1

Sequence conflict

510

1

C → Y in AAB87640. Ref.1

Sequence conflict

521

1

A → L in AAB87640. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

522

Helix Strand Turn

Details...

Helix

108 – 114

7

Beta strand

119 – 121

3

Helix

126 – 136

11

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 2, 2002. Version 2. Checksum: 08975A26D0B21857	FASTA	522	58,449
	10 20 30 40 50 60 MASSRASSTQ ATKTKAPDDL VAPVVKKPHI YYGSLEEKER ERLAKGESGI LGKDGLKAGI 70 80 90 100 110 120 EAGNINITSG EVFEIEEHIS ERQAEVLAEF ERRKRARQIN VSTDDSEVKA CLRALGEPIT 130 140 150 160 170 180 LFGEGPAERR ERLRNILSVV GTDALKKTKK DDEKSKKSKE EYQQTWYHEG PNSLKVARLW 190 200 210 220 230 240 IANYSLPRAM KRLEEARLHK EIPETTRTSQ MQELHKSLRS LNNFCSQIGD DRPISYCHFS 250 260 270 280 290 300 PNSKMLATAC WSGLCKLWSV PDCNLLHTLR GHNTNVGAIV FHPKSTVSLD PKDVNLASCA 310 320 330 340 350 360 ADGSVKLWSL DSDEPVADIE GHTVRVARVM WHPSGRFLGT TCYDRSWRLW DLEAQEEILH 370 380 390 400 410 420 QEGHSMGVYD IAFHQDGSLA GTGGLDAFGR VWDLRTGRCI MFLEGHLKEI YGINFSPNGY 430 440 450 460 470 480 HIATGSGDNT CKVWDLRQRR CVYTIPAHQN LVTGVKFEPI HGNFLLTGAY DNTAKIWTHP 490 500 510 520 GWSPLKTLAG HEGKVMGLDI SSDGQLIATC SYDRTFKLWM AE
	Isoform 2 [UniParc]. Checksum: B4EF92D9E12C9188	FASTA	521	58,321
	10 20 30 40 50 60 MASSRASSTA TKTKAPDDLV APVVKKPHIY YGSLEEKERE RLAKGESGIL GKDGLKAGIE 70 80 90 100 110 120 AGNINITSGE VFEIEEHISE RQAEVLAEFE RRKRARQINV STDDSEVKAC LRALGEPITL 130 140 150 160 170 180 FGEGPAERRE RLRNILSVVG TDALKKTKKD DEKSKKSKEE YQQTWYHEGP NSLKVARLWI 190 200 210 220 230 240 ANYSLPRAMK RLEEARLHKE IPETTRTSQM QELHKSLRSL NNFCSQIGDD RPISYCHFSP 250 260 270 280 290 300 NSKMLATACW SGLCKLWSVP DCNLLHTLRG HNTNVGAIVF HPKSTVSLDP KDVNLASCAA 310 320 330 340 350 360 DGSVKLWSLD SDEPVADIEG HTVRVARVMW HPSGRFLGTT CYDRSWRLWD LEAQEEILHQ 370 380 390 400 410 420 EGHSMGVYDI AFHQDGSLAG TGGLDAFGRV WDLRTGRCIM FLEGHLKEIY GINFSPNGYH 430 440 450 460 470 480 IATGSGDNTC KVWDLRQRRC VYTIPAHQNL VTGVKFEPIH GNFLLTGAYD NTAKIWTHPG 490 500 510 520 WSPLKTLAGH EGKVMGLDIS SDGQLIATCS YDRTFKLWMA E

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The human U4/U6 snRNP contains 60 and 90kD proteins that are structurally homologous to the yeast splicing factors Prp4p and Prp3p." Lauber J., Plessel G., Prehn S., Will C.L., Fabrizio P., Groning K., Lane W.S., Luehrmann R. RNA 3:926-941(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 2).
[2]	"A new cyclophilin and the human homologues of yeast Prp3 and Prp4 form a complex associated with U4/U6 snRNPs." Horowitz D.S., Kobayashi R., Krainer A.R. RNA 3:1374-1387(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROTEIN SEQUENCE OF 28-38; 58-85; 95-106; 193-200 AND 457-472, INTERACTION WITH U4/U5/U6 SNRNPS.
[3]	"Identification and characterization of human genes encoding Hprp3p and Hprp4p, interacting components of the spliceosome." Wang A., Forman-Kay J., Luo Y., Luo M., Chow Y.-H., Plumb J., Friesen J.D., Tsui L.-C., Heng H.H.Q., Woolford J.L. Jr., Hu J. Hum. Mol. Genet. 6:2117-2126(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), INTERACTION WITH PRPF3 AND U4/U5/U6 SNRNPS.
[4]	"DNA sequence and analysis of human chromosome 9." Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I. Nature 429:369-374(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	"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] (ISOFORMS 1 AND 2). Tissue: Colon and Ovary.
[7]	"A human protein required for the second step of pre-mRNA splicing is functionally related to a yeast splicing factor." Horowitz D.S., Krainer A.R. Genes Dev. 11:139-151(1997) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PRPF18.
[8]	"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.
[9]	"Lysine acetylation targets protein complexes and co-regulates major cellular functions." Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M. Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-27, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]	"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].
[11]	"Crystal structure of a complex between human spliceosomal cyclophilin H and a U4/U6 snRNP-60K peptide." Reidt U., Wahl M.C., Fasshauer D., Horowitz D.S., Luehrmann R., Ficner R. J. Mol. Biol. 331:45-56(2003) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 107-137 IN COMPLEX WITH PPIH.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF001687 Genomic DNA. Translation: AAB87640.1.
AF016369 mRNA. Translation: AAC51925.1.
U82756 mRNA. Translation: AAC02261.1.
AL449305 Genomic DNA. Translation: CAI10968.1.
CH471090 Genomic DNA. Translation: EAW87362.1.
BC001588 mRNA. Translation: AAH01588.1.
BC007424 mRNA. Translation: AAH07424.1.

CCDS

CCDS59142.1. [O43172-2]
CCDS6791.1. [O43172-1]

RefSeq

NP_001231855.1. NM_001244926.1. [O43172-2]
NP_004688.2. NM_004697.4. [O43172-1]

UniGene

Hs.744014.

3D structure databases

PDBe
RCSB-PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1MZW	X-ray	2.00	B	107-137	[»]

ProteinModelPortal

O43172.

SMR

O43172. Positions 107-137, 239-519.

ModBase

Search...

MobiDB

Search...

Protein-protein interaction databases

BioGrid

114576. 67 interactions.

IntAct

O43172. 35 interactions.

MINT

MINT-270624.

STRING

9606.ENSP00000363313.

Chemistry

BindingDB

O43172.

ChEMBL

CHEMBL1163119.

PTM databases

PhosphoSite

O43172.

Proteomic databases

MaxQB

O43172.

PaxDb

O43172.

PRIDE

O43172.

Protocols and materials databases

DNASU

9128.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000374198; ENSP00000363313; ENSG00000136875. [O43172-1]
ENST00000374199; ENSP00000363315; ENSG00000136875. [O43172-2]

GeneID

9128.

KEGG

hsa:9128.

UCSC

uc004bgx.3. human. [O43172-1]

Organism-specific databases

CTD

9128.

GeneCards

GC09P116037.

HGNC

HGNC:17349. PRPF4.

HPA

HPA021794.
HPA022248.

MIM

607795. gene.

neXtProt

NX_O43172.

PharmGKB

PA38448.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG2319.

HOGENOM

HOG000157615.

HOVERGEN

HBG030892.

InParanoid

O43172.

KO

K12662.

OMA

HPSRQAY.

OrthoDB

EOG7P5T0Z.

PhylomeDB

O43172.

TreeFam

TF314922.

Enzyme and pathway databases

Reactome

REACT_71. Gene Expression.

SignaLink

O43172.

Gene expression databases

ArrayExpress

O43172.

Bgee

O43172.

CleanEx

HS_PRPF4.

Genevestigator

O43172.

Family and domain databases

Gene3D

2.130.10.10. 1 hit.

InterPro

IPR020472. G-protein_beta_WD-40_rep.
IPR027106. Prp4.
IPR014906. PRP4-like.
IPR003648. SFM.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]

PANTHER

PTHR19846. PTHR19846. 1 hit.

Pfam

PF08799. PRP4. 1 hit.
PF00400. WD40. 7 hits.
[Graphical view]

PRINTS

PR00320. GPROTEINBRPT.

SMART

SM00500. SFM. 1 hit.
SM00320. WD40. 7 hits.
[Graphical view]

SUPFAM

SSF50978. SSF50978. 1 hit.

PROSITE

PS00678. WD_REPEATS_1. 2 hits.
PS50082. WD_REPEATS_2. 6 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

O43172.

GeneWiki

PRPF4.

GenomeRNAi

9128.

NextBio

34217.

PRO

O43172.

SOURCE

Search...

Entry information

Entry name

PRP4_HUMAN

Accession

Primary (citable) accession number: O43172
Secondary accession number(s): O43445 , O43864, Q5T1M8, Q96DG2, Q96IK4

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 2, 2002
Last sequence update:	May 2, 2002
Last modified:	July 9, 2014
This is version 144 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

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.