UniProtKB - O43395 (PRPF3_HUMAN)
U4/U6 small nuclear ribonucleoprotein Prp3
PRPF3
Functioni
Plays role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex).
1 Publication2 PublicationsGO - Molecular functioni
- identical protein binding Source: IntAct
- RNA binding Source: UniProtKB
GO - Biological processi
- mRNA processing Source: ProtInc
- mRNA splicing, via spliceosome Source: UniProtKB
- RNA splicing Source: ProtInc
- RNA splicing, via transesterification reactions Source: UniProtKB
- spliceosomal tri-snRNP complex assembly Source: UniProtKB
Keywordsi
Biological process | mRNA processing, mRNA splicing |
Enzyme and pathway databases
PathwayCommonsi | O43395 |
Reactomei | R-HSA-72163, mRNA Splicing - Major Pathway |
SignaLinki | O43395 |
SIGNORi | O43395 |
Names & Taxonomyi
Protein namesi | Recommended name: U4/U6 small nuclear ribonucleoprotein Prp3Alternative name(s): Pre-mRNA-splicing factor 3 Short name: hPrp3 U4/U6 snRNP 90 kDa protein |
Gene namesi | Name:PRPF3 Synonyms:HPRP31 Publication, PRP3 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
HGNCi | HGNC:17348, PRPF3 |
MIMi | 607301, gene |
neXtProti | NX_O43395 |
VEuPathDBi | HostDB:ENSG00000117360 |
Subcellular locationi
Nucleus
- Nucleus 5 Publications
- Nucleus speckle
Cytosol
- cytosol Source: HPA
Nucleus
- Cajal body Source: BHF-UCL
- nuclear speck Source: HPA
- nucleoplasm Source: HPA
- nucleus Source: UniProtKB
- spliceosomal complex Source: UniProtKB
- U2-type precatalytic spliceosome Source: UniProtKB
- U4/U6 x U5 tri-snRNP complex Source: UniProtKB
Keywords - Cellular componenti
Nucleus, SpliceosomePathology & Biotechi
Involvement in diseasei
Retinitis pigmentosa 18 (RP18)3 Publications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_046735 | 493 | P → S in RP18. 1 PublicationCorresponds to variant dbSNP:rs121434242EnsemblClinVar. | 1 | |
Natural variantiVAR_016877 | 494 | T → M in RP18; reduces phosphorylation; impairs binding to PRPF4; impairs self-association; affects interaction with the U4/U5/U6 tri-snRNP complex; does not affect global pre-mRNA splicing. 3 PublicationsCorresponds to variant dbSNP:rs121434241EnsemblClinVar. | 1 |
Keywords - Diseasei
Disease variant, Retinitis pigmentosaOrganism-specific databases
DisGeNETi | 9129 |
GeneReviewsi | PRPF3 |
MalaCardsi | PRPF3 |
MIMi | 601414, phenotype |
OpenTargetsi | ENSG00000117360 |
Orphaneti | 791, Retinitis pigmentosa |
PharmGKBi | PA134892509 |
Miscellaneous databases
Pharosi | O43395, Tbio |
Genetic variation databases
BioMutai | PRPF3 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000097044 | 1 – 683 | U4/U6 small nuclear ribonucleoprotein Prp3Add BLAST | 683 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Cross-linki | 139 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Modified residuei | 164 | PhosphoserineCombined sources | 1 | |
Modified residuei | 167 | PhosphothreonineCombined sources | 1 | |
Cross-linki | 244 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Cross-linki | 252 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources | ||
Modified residuei | 619 | PhosphoserineCombined sources | 1 |
Post-translational modificationi
Keywords - PTMi
Isopeptide bond, Phosphoprotein, Ubl conjugationProteomic databases
EPDi | O43395 |
jPOSTi | O43395 |
MassIVEi | O43395 |
MaxQBi | O43395 |
PaxDbi | O43395 |
PeptideAtlasi | O43395 |
PRIDEi | O43395 |
ProteomicsDBi | 48921 [O43395-1] 5058 |
PTM databases
GlyGeni | O43395, 3 sites, 1 O-linked glycan (3 sites) |
iPTMneti | O43395 |
MetOSitei | O43395 |
PhosphoSitePlusi | O43395 |
SwissPalmi | O43395 |
Expressioni
Tissue specificityi
Gene expression databases
Bgeei | ENSG00000117360, Expressed in left lobe of thyroid gland and 239 other tissues |
Genevisiblei | O43395, HS |
Organism-specific databases
HPAi | ENSG00000117360, Low tissue specificity |
Interactioni
Subunit structurei
Component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166).
Component of the U4/U6-U5 tri-snRNP complex, a building block of the precatalytic spliceosome (spliceosome B complex) (PubMed:9328476, PubMed:9404889, PubMed:28781166, PubMed:26912367, PubMed:17932117). The U4/U6-U5 tri-snRNP complex is composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:16723661, PubMed:26912367).
Interacts directly with PRPF4 (PubMed:9328476, PubMed:9404889, PubMed:17932117).
Part of a heteromeric complex containing PPIH, PRPF3 and PRPF4 that is stable in the absence of RNA (PubMed:9404889).
Interacts with SART3; the interaction is direct and recruits the deubiquitinase USP4 to PRPF3 (PubMed:15314151, PubMed:20595234).
Interacts with PRPF19.
Interacts ('Lys-63'-linked polyubiquitinated) with PRPF8 (via the MPN (JAB/Mov34) domain); may stabilize the U4/U6-U5 tri-snRNP complex (PubMed:20595234).
Interacts with ERCC6 (PubMed:26030138).
9 PublicationsBinary interactionsi
O43395
GO - Molecular functioni
- identical protein binding Source: IntAct
Protein-protein interaction databases
BioGRIDi | 114577, 220 interactors |
CORUMi | O43395 |
DIPi | DIP-34508N |
IntActi | O43395, 100 interactors |
MINTi | O43395 |
STRINGi | 9606.ENSP00000315379 |
Miscellaneous databases
RNActi | O43395, protein |
Structurei
Secondary structure
3D structure databases
SMRi | O43395 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | O43395 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 1 – 87 | PWIPROSITE-ProRule annotationAdd BLAST | 87 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 73 – 135 | DisorderedSequence analysisAdd BLAST | 63 | |
Regioni | 153 – 183 | DisorderedSequence analysisAdd BLAST | 31 | |
Regioni | 416 – 550 | Mediates interaction with SART31 PublicationAdd BLAST | 135 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 73 – 122 | Basic and acidic residuesSequence analysisAdd BLAST | 50 |
Phylogenomic databases
eggNOGi | KOG2769, Eukaryota |
GeneTreei | ENSGT00390000011497 |
HOGENOMi | CLU_015750_3_0_1 |
InParanoidi | O43395 |
OMAi | AQKPTVR |
OrthoDBi | 1322299at2759 |
PhylomeDBi | O43395 |
TreeFami | TF313082 |
Family and domain databases
InterProi | View protein in InterPro IPR010541, DUF1115 IPR013881, Pre-mRNA_splic_Prp3 IPR027104, Prp3 IPR002483, PWI_dom IPR036483, PWI_dom_sf |
PANTHERi | PTHR14212, PTHR14212, 1 hit |
Pfami | View protein in Pfam PF06544, DUF1115, 1 hit PF08572, PRP3, 1 hit PF01480, PWI, 1 hit |
SMARTi | View protein in SMART SM00311, PWI, 1 hit |
SUPFAMi | SSF101233, SSF101233, 1 hit |
PROSITEi | View protein in PROSITE PS51025, PWI, 1 hit |
s (2)i Sequence
Sequence statusi: Complete.
This entry describes 2 produced by isoformsialternative splicing. AlignAdd to basketThis isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
10 20 30 40 50
MALSKRELDE LKPWIEKTVK RVLGFSEPTV VTAALNCVGK GMDKKKAADH
60 70 80 90 100
LKPFLDDSTL RFVDKLFEAV EEGRSSRHSK SSSDRSRKRE LKEVFGDDSE
110 120 130 140 150
ISKESSGVKK RRIPRFEEVE EEPEVIPGPP SESPGMLTKL QIKQMMEAAT
160 170 180 190 200
RQIEERKKQL SFISPPTPQP KTPSSSQPER LPIGNTIQPS QAATFMNDAI
210 220 230 240 250
EKARKAAELQ ARIQAQLALK PGLIGNANMV GLANLHAMGI APPKVELKDQ
260 270 280 290 300
TKPTPLILDE QGRTVDATGK EIELTHRMPT LKANIRAVKR EQFKQQLKEK
310 320 330 340 350
PSEDMESNTF FDPRVSIAPS QRQRRTFKFH DKGKFEKIAQ RLRTKAQLEK
360 370 380 390 400
LQAEISQAAR KTGIHTSTRL ALIAPKKELK EGDIPEIEWW DSYIIPNGFD
410 420 430 440 450
LTEENPKRED YFGITNLVEH PAQLNPPVDN DTPVTLGVYL TKKEQKKLRR
460 470 480 490 500
QTRREAQKEL QEKVRLGLMP PPEPKVRISN LMRVLGTEAV QDPTKVEAHV
510 520 530 540 550
RAQMAKRQKA HEEANAARKL TAEQRKVKKI KKLKEDISQG VHISVYRVRN
560 570 580 590 600
LSNPAKKFKI EANAGQLYLT GVVVLHKDVN VVVVEGGPKA QKKFKRLMLH
610 620 630 640 650
RIKWDEQTSN TKGDDDEESD EEAVKKTNKC VLVWEGTAKD RSFGEMKFKQ
660 670 680
CPTENMAREH FKKHGAEHYW DLALSESVLE STD
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 142 | I → T in AAC09069 (PubMed:9328476).Curated | 1 | |
Sequence conflicti | 273 – 274 | EL → SV in AAC09069 (PubMed:9328476).Curated | 2 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_051286 | 12 | K → N. Corresponds to variant dbSNP:rs12736964Ensembl. | 1 | |
Natural variantiVAR_046735 | 493 | P → S in RP18. 1 PublicationCorresponds to variant dbSNP:rs121434242EnsemblClinVar. | 1 | |
Natural variantiVAR_016877 | 494 | T → M in RP18; reduces phosphorylation; impairs binding to PRPF4; impairs self-association; affects interaction with the U4/U5/U6 tri-snRNP complex; does not affect global pre-mRNA splicing. 3 PublicationsCorresponds to variant dbSNP:rs121434241EnsemblClinVar. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_056265 | 1 – 135 | Missing in isoform 2. 1 PublicationAdd BLAST | 135 | |
Alternative sequenceiVSP_056266 | 402 – 416 | TEENP…FGITN → GKSQERRLFWNHKSC in isoform 2. 1 PublicationAdd BLAST | 15 | |
Alternative sequenceiVSP_056267 | 417 – 683 | Missing in isoform 2. 1 PublicationAdd BLAST | 267 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF001947 mRNA Translation: AAC09069.1 AF016370 mRNA Translation: AAC51926.1 AK299980 mRNA Translation: BAG61801.1 AL611942 Genomic DNA No translation available. CH471121 Genomic DNA Translation: EAW53556.1 BC000184 mRNA Translation: AAH00184.1 BC001954 mRNA Translation: AAH01954.1 |
CCDSi | CCDS951.1 [O43395-1] |
PIRi | T50839 T50840 |
RefSeqi | NP_004689.1, NM_004698.2 [O43395-1] |
Genome annotation databases
Ensembli | ENST00000324862; ENSP00000315379; ENSG00000117360 |
GeneIDi | 9129 |
KEGGi | hsa:9129 |
MANE-Selecti | ENST00000324862.7; ENSP00000315379.6; NM_004698.4; NP_004689.1 |
UCSCi | uc001eum.5, human [O43395-1] |
Keywords - Coding sequence diversityi
Alternative splicingSimilar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF001947 mRNA Translation: AAC09069.1 AF016370 mRNA Translation: AAC51926.1 AK299980 mRNA Translation: BAG61801.1 AL611942 Genomic DNA No translation available. CH471121 Genomic DNA Translation: EAW53556.1 BC000184 mRNA Translation: AAH00184.1 BC001954 mRNA Translation: AAH01954.1 |
CCDSi | CCDS951.1 [O43395-1] |
PIRi | T50839 T50840 |
RefSeqi | NP_004689.1, NM_004698.2 [O43395-1] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1X4Q | NMR | - | A | 1-79 | [»] | |
3JCR | electron microscopy | 7.00 | K | 1-683 | [»] | |
5O9Z | electron microscopy | 4.50 | E | 1-683 | [»] | |
6AH0 | electron microscopy | 5.70 | J | 1-683 | [»] | |
6AHD | electron microscopy | 3.80 | J | 1-683 | [»] | |
6QW6 | electron microscopy | 2.92 | 4A | 1-683 | [»] | |
6QX9 | electron microscopy | 3.28 | 4A | 1-683 | [»] | |
SMRi | O43395 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 114577, 220 interactors |
CORUMi | O43395 |
DIPi | DIP-34508N |
IntActi | O43395, 100 interactors |
MINTi | O43395 |
STRINGi | 9606.ENSP00000315379 |
PTM databases
GlyGeni | O43395, 3 sites, 1 O-linked glycan (3 sites) |
iPTMneti | O43395 |
MetOSitei | O43395 |
PhosphoSitePlusi | O43395 |
SwissPalmi | O43395 |
Genetic variation databases
BioMutai | PRPF3 |
Proteomic databases
EPDi | O43395 |
jPOSTi | O43395 |
MassIVEi | O43395 |
MaxQBi | O43395 |
PaxDbi | O43395 |
PeptideAtlasi | O43395 |
PRIDEi | O43395 |
ProteomicsDBi | 48921 [O43395-1] 5058 |
Protocols and materials databases
Antibodypediai | 20281, 183 antibodies from 31 providers |
DNASUi | 9129 |
Genome annotation databases
Ensembli | ENST00000324862; ENSP00000315379; ENSG00000117360 |
GeneIDi | 9129 |
KEGGi | hsa:9129 |
MANE-Selecti | ENST00000324862.7; ENSP00000315379.6; NM_004698.4; NP_004689.1 |
UCSCi | uc001eum.5, human [O43395-1] |
Organism-specific databases
CTDi | 9129 |
DisGeNETi | 9129 |
GeneCardsi | PRPF3 |
GeneReviewsi | PRPF3 |
HGNCi | HGNC:17348, PRPF3 |
HPAi | ENSG00000117360, Low tissue specificity |
MalaCardsi | PRPF3 |
MIMi | 601414, phenotype 607301, gene |
neXtProti | NX_O43395 |
OpenTargetsi | ENSG00000117360 |
Orphaneti | 791, Retinitis pigmentosa |
PharmGKBi | PA134892509 |
VEuPathDBi | HostDB:ENSG00000117360 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG2769, Eukaryota |
GeneTreei | ENSGT00390000011497 |
HOGENOMi | CLU_015750_3_0_1 |
InParanoidi | O43395 |
OMAi | AQKPTVR |
OrthoDBi | 1322299at2759 |
PhylomeDBi | O43395 |
TreeFami | TF313082 |
Enzyme and pathway databases
PathwayCommonsi | O43395 |
Reactomei | R-HSA-72163, mRNA Splicing - Major Pathway |
SignaLinki | O43395 |
SIGNORi | O43395 |
Miscellaneous databases
BioGRID-ORCSi | 9129, 640 hits in 1048 CRISPR screens |
ChiTaRSi | PRPF3, human |
EvolutionaryTracei | O43395 |
GeneWikii | PRPF3 |
GenomeRNAii | 9129 |
Pharosi | O43395, Tbio |
PROi | PR:O43395 |
RNActi | O43395, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000117360, Expressed in left lobe of thyroid gland and 239 other tissues |
Genevisiblei | O43395, HS |
Family and domain databases
InterProi | View protein in InterPro IPR010541, DUF1115 IPR013881, Pre-mRNA_splic_Prp3 IPR027104, Prp3 IPR002483, PWI_dom IPR036483, PWI_dom_sf |
PANTHERi | PTHR14212, PTHR14212, 1 hit |
Pfami | View protein in Pfam PF06544, DUF1115, 1 hit PF08572, PRP3, 1 hit PF01480, PWI, 1 hit |
SMARTi | View protein in SMART SM00311, PWI, 1 hit |
SUPFAMi | SSF101233, SSF101233, 1 hit |
PROSITEi | View protein in PROSITE PS51025, PWI, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | PRPF3_HUMAN | |
Accessioni | O43395Primary (citable) accession number: O43395 Secondary accession number(s): B4DSY9, O43446, Q5VT54 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | September 26, 2003 |
Last sequence update: | September 26, 2003 | |
Last modified: | February 23, 2022 | |
This is version 204 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | 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. |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- Human chromosome 1
Human chromosome 1: entries, gene names and cross-references to MIM - Human entries with genetic variants
List of human entries with genetic variants - Human variants curated from literature reports
Index of human variants curated from literature reports - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references