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Protein

Small nuclear ribonucleoprotein F

Gene

SNRPF

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

Functioni

Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. As part of the U7 snRNP it is involved in histone 3'-end processing.2 Publications

GO - Molecular functioni

  • RNA binding Source: UniProtKB

GO - Biological processi

  • histone mRNA metabolic process Source: Reactome
  • mitophagy in response to mitochondrial depolarization Source: ParkinsonsUK-UCL
  • mRNA splicing, via spliceosome Source: UniProtKB
  • nuclear import Source: Reactome
  • RNA splicing Source: UniProtKB
  • spliceosomal snRNP assembly Source: UniProtKB
  • termination of RNA polymerase II transcription Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-111367. SLBP independent Processing of Histone Pre-mRNAs.
R-HSA-191859. snRNP Assembly.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.
R-HSA-77588. SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs.

Names & Taxonomyi

Protein namesi
Recommended name:
Small nuclear ribonucleoprotein F
Short name:
snRNP-F
Alternative name(s):
Sm protein F
Short name:
Sm-F
Short name:
SmF
Gene namesi
Name:SNRPF
Synonyms:PBSCF
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:11162. SNRPF.

Subcellular locationi

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: UniProtKB
  • cytosol Source: UniProtKB
  • methylosome Source: UniProtKB
  • nucleoplasm Source: Reactome
  • pICln-Sm protein complex Source: UniProtKB
  • small nuclear ribonucleoprotein complex Source: UniProtKB
  • small nucleolar ribonucleoprotein complex Source: InterPro
  • SMN-Sm protein complex Source: UniProtKB
  • spliceosomal complex Source: UniProtKB
  • U12-type spliceosomal complex Source: UniProtKB
  • U1 snRNP Source: UniProtKB
  • U4 snRNP Source: UniProtKB
  • U7 snRNP Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA36003.

Polymorphism and mutation databases

BioMutaiSNRPF.
DMDMi61237391.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 8685Small nuclear ribonucleoprotein FPRO_0000125536Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP62306.
MaxQBiP62306.
PaxDbiP62306.
PeptideAtlasiP62306.
PRIDEiP62306.
TopDownProteomicsiP62306.

PTM databases

iPTMnetiP62306.
PhosphoSiteiP62306.

Miscellaneous databases

PMAP-CutDBP62306.

Expressioni

Gene expression databases

BgeeiENSG00000139343.
CleanExiHS_SNRPF.
ExpressionAtlasiP62306. baseline and differential.
GenevisibleiP62306. HS.

Interactioni

Subunit structurei

U1 snRNP is for instance composed of the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Component of the heptameric ring U7 snRNP complex, or U7 Sm protein core complex, at least composed of LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF, SNRPG and U7 snRNA. Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG; catalyzes core snRNPs assembly. Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CLNS1AP541054EBI-356900,EBI-724693
COILP384323EBI-356900,EBI-945751
HOMER3B2RA103EBI-356900,EBI-10175777
IKZF1Q134223EBI-356900,EBI-745305
LNX1Q8TBB13EBI-356900,EBI-739832
LSM5Q9Y4Y96EBI-356900,EBI-373007
SNRPEP623044EBI-356900,EBI-348082

Protein-protein interaction databases

BioGridi112520. 151 interactions.
DIPiDIP-31221N.
IntActiP62306. 33 interactions.
MINTiMINT-1137229.
STRINGi9606.ENSP00000266735.

Structurei

Secondary structure

1
86
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi7 – 148Combined sources
Beta strandi17 – 237Combined sources
Beta strandi28 – 369Combined sources
Beta strandi42 – 5110Combined sources
Beta strandi54 – 6411Combined sources
Helixi66 – 683Combined sources
Beta strandi69 – 746Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3CW1X-ray5.491/2/F/Z1-86[»]
3JCRelectron microscopy7.00T/t1-86[»]
3PGWX-ray4.40F/I1-86[»]
3S6NX-ray2.50F1-86[»]
4F7UX-ray1.90F/I1-86[»]
4PJOX-ray3.30F/T/f/t1-75[»]
4V98X-ray3.10AD/AL/AT/Ab/Aj/Ar/Az/BD/BL/BT/Bb/Bj/Br/Bz/CD/CL/CT/Cb/Cj/Cr1-86[»]
4WZJX-ray3.60AF/AM/AT/BF/BM/BT/CF/CM/CT/DF/DM/DT1-86[»]
ProteinModelPortaliP62306.
SMRiP62306. Positions 3-76.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62306.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG3482. Eukaryota.
ENOG4111W47. LUCA.
GeneTreeiENSGT00730000110856.
HOVERGENiHBG052369.
InParanoidiP62306.
KOiK11098.
OMAiKWGHEYK.
PhylomeDBiP62306.
TreeFamiTF314481.

Family and domain databases

InterProiIPR016487. Lsm6/sSmF.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PfamiPF01423. LSM. 1 hit.
[Graphical view]
PIRSFiPIRSF006609. snRNP_SmF. 1 hit.
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P62306-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLPLNPKPF LNGLTGKPVM VKLKWGMEYK GYLVSVDGYM NMQLANTEEY
60 70 80
IDGALSGHLG EVLIRCNNVL YIRGVEEEEE DGEMRE
Length:86
Mass (Da):9,725
Last modified:July 5, 2004 - v1
Checksum:i416B88D575DAE58A
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti86 – 861E → D in CAG33032 (Ref. 2) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X85372 mRNA. Translation: CAA59688.1.
CR456751 mRNA. Translation: CAG33032.1.
AK311752 mRNA. Translation: BAG34695.1.
CH471054 Genomic DNA. Translation: EAW97548.1.
BC002505 mRNA. Translation: AAH02505.3.
BC063397 mRNA. Translation: AAH63397.2.
BC128452 mRNA. Translation: AAI28453.1.
BC128453 mRNA. Translation: AAI28454.1.
CCDSiCCDS9055.1.
PIRiS55053.
RefSeqiNP_003086.1. NM_003095.2.
UniGeneiHs.105465.

Genome annotation databases

EnsembliENST00000266735; ENSP00000266735; ENSG00000139343.
GeneIDi6636.
KEGGihsa:6636.
UCSCiuc001tej.5. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X85372 mRNA. Translation: CAA59688.1.
CR456751 mRNA. Translation: CAG33032.1.
AK311752 mRNA. Translation: BAG34695.1.
CH471054 Genomic DNA. Translation: EAW97548.1.
BC002505 mRNA. Translation: AAH02505.3.
BC063397 mRNA. Translation: AAH63397.2.
BC128452 mRNA. Translation: AAI28453.1.
BC128453 mRNA. Translation: AAI28454.1.
CCDSiCCDS9055.1.
PIRiS55053.
RefSeqiNP_003086.1. NM_003095.2.
UniGeneiHs.105465.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3CW1X-ray5.491/2/F/Z1-86[»]
3JCRelectron microscopy7.00T/t1-86[»]
3PGWX-ray4.40F/I1-86[»]
3S6NX-ray2.50F1-86[»]
4F7UX-ray1.90F/I1-86[»]
4PJOX-ray3.30F/T/f/t1-75[»]
4V98X-ray3.10AD/AL/AT/Ab/Aj/Ar/Az/BD/BL/BT/Bb/Bj/Br/Bz/CD/CL/CT/Cb/Cj/Cr1-86[»]
4WZJX-ray3.60AF/AM/AT/BF/BM/BT/CF/CM/CT/DF/DM/DT1-86[»]
ProteinModelPortaliP62306.
SMRiP62306. Positions 3-76.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi112520. 151 interactions.
DIPiDIP-31221N.
IntActiP62306. 33 interactions.
MINTiMINT-1137229.
STRINGi9606.ENSP00000266735.

PTM databases

iPTMnetiP62306.
PhosphoSiteiP62306.

Polymorphism and mutation databases

BioMutaiSNRPF.
DMDMi61237391.

Proteomic databases

EPDiP62306.
MaxQBiP62306.
PaxDbiP62306.
PeptideAtlasiP62306.
PRIDEiP62306.
TopDownProteomicsiP62306.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000266735; ENSP00000266735; ENSG00000139343.
GeneIDi6636.
KEGGihsa:6636.
UCSCiuc001tej.5. human.

Organism-specific databases

CTDi6636.
GeneCardsiSNRPF.
HGNCiHGNC:11162. SNRPF.
MIMi603541. gene.
neXtProtiNX_P62306.
PharmGKBiPA36003.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3482. Eukaryota.
ENOG4111W47. LUCA.
GeneTreeiENSGT00730000110856.
HOVERGENiHBG052369.
InParanoidiP62306.
KOiK11098.
OMAiKWGHEYK.
PhylomeDBiP62306.
TreeFamiTF314481.

Enzyme and pathway databases

ReactomeiR-HSA-109688. Cleavage of Growing Transcript in the Termination Region.
R-HSA-111367. SLBP independent Processing of Histone Pre-mRNAs.
R-HSA-191859. snRNP Assembly.
R-HSA-72163. mRNA Splicing - Major Pathway.
R-HSA-72165. mRNA Splicing - Minor Pathway.
R-HSA-77588. SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs.

Miscellaneous databases

ChiTaRSiSNRPF. human.
EvolutionaryTraceiP62306.
GeneWikiiSmall_nuclear_ribonucleoprotein_polypeptide_F.
GenomeRNAii6636.
PMAP-CutDBP62306.
PROiP62306.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000139343.
CleanExiHS_SNRPF.
ExpressionAtlasiP62306. baseline and differential.
GenevisibleiP62306. HS.

Family and domain databases

InterProiIPR016487. Lsm6/sSmF.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PfamiPF01423. LSM. 1 hit.
[Graphical view]
PIRSFiPIRSF006609. snRNP_SmF. 1 hit.
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRUXF_HUMAN
AccessioniPrimary (citable) accession number: P62306
Secondary accession number(s): A2VCR2
, B2R498, Q15356, Q6IBQ1, Q6P4I0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: September 7, 2016
This is version 125 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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 one 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.