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P62306 (RUXF_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 102. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | 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:
Small nuclear ribonucleoprotein F

Short name=snRNP-F
Alternative name(s):
Sm protein F
Short name=Sm-F
Short name=SmF
Gene names
Name:SNRPF
Synonyms:PBSCF
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length86 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 an 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. Ref.10 Ref.14

Subunit structure

U1 snRNP is for instance composed of the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in an 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. Ref.7 Ref.8 Ref.9 Ref.10 Ref.14

Subcellular location

Cytoplasmcytosol. Nucleus. Note: SMN-mediated assembly into core snRNPs occurs in the cytosol before SMN-mediated transport to the nucleus to be included in spliceosomes. Ref.10

Sequence similarities

Belongs to the snRNP Sm proteins family. SmF/LSm6 subfamily.

Ontologies

Keywords
   Biological processmRNA processing
mRNA splicing
   Cellular componentCytoplasm
Nucleus
Spliceosome
   LigandRNA-binding
   Molecular functionRibonucleoprotein
   PTMAcetylation
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processRNA metabolic process

Traceable author statement. Source: Reactome

RNA splicing

Inferred from mutant phenotype Ref.1. Source: UniProtKB

gene expression

Traceable author statement. Source: Reactome

histone mRNA metabolic process

Traceable author statement. Source: Reactome

mRNA 3'-end processing

Traceable author statement. Source: Reactome

mRNA splicing, via spliceosome

Inferred by curator Ref.8. Source: UniProtKB

ncRNA metabolic process

Traceable author statement. Source: Reactome

spliceosomal snRNP assembly

Inferred from direct assay Ref.10. Source: UniProtKB

termination of RNA polymerase II transcription

Traceable author statement. Source: Reactome

transcription from RNA polymerase II promoter

Traceable author statement. Source: Reactome

   Cellular_componentSMN-Sm protein complex

Inferred from direct assay Ref.10. Source: UniProtKB

U1 snRNP

Inferred from direct assay PubMed 21113136. Source: UniProtKB

U12-type spliceosomal complex

Inferred from direct assay Ref.9. Source: UniProtKB

U4 snRNP

Inferred from direct assay Ref.13. Source: UniProtKB

U7 snRNP

Inferred from direct assay Ref.7. Source: UniProtKB

catalytic step 2 spliceosome

Inferred from direct assay Ref.8. Source: UniProtKB

cytosol

Inferred from direct assay Ref.10. Source: UniProtKB

methylosome

Inferred from direct assay Ref.10. Source: UniProtKB

nucleoplasm

Traceable author statement. Source: Reactome

pICln-Sm protein complex

Inferred from direct assay Ref.10. Source: UniProtKB

small nuclear ribonucleoprotein complex

Inferred from direct assay Ref.8. Source: UniProtKB

spliceosomal complex

Inferred from direct assay Ref.1. Source: UniProtKB

   Molecular_functionRNA binding

Inferred from mutant phenotype Ref.1. Source: UniProtKB

protein binding

Inferred from physical interaction Ref.10PubMed 22365833PubMed 9417867. Source: IntAct

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

CLNS1AP541054EBI-356900,EBI-724693
SNRPEP623044EBI-356900,EBI-348082

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.6
Chain2 – 8685Small nuclear ribonucleoprotein F
PRO_0000125536

Amino acid modifications

Modified residue21N-acetylserine Ref.6

Experimental info

Sequence conflict861E → D in CAG33032. Ref.2

Secondary structure

.............. 86
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P62306 [UniParc].

Last modified July 5, 2004. Version 1.
Checksum: 416B88D575DAE58A

FASTA869,725
        10         20         30         40         50         60 
MSLPLNPKPF LNGLTGKPVM VKLKWGMEYK GYLVSVDGYM NMQLANTEEY IDGALSGHLG 

        70         80 
EVLIRCNNVL YIRGVEEEEE DGEMRE 

« Hide

References

« Hide 'large scale' references
[1]"snRNP Sm proteins share two evolutionarily conserved sequence motifs which are involved in Sm protein-protein interactions."
Hermann H., Fabrizio P., Raker V.A., Foulaki K., Hornig H., Brahms H., Luehrmann R.
EMBO J. 14:2076-2088(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Tissue: Cervix carcinoma.
[2]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[3]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Amygdala.
[4]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. expand/collapse author list , 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].
[5]"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: Colon.
[6]Bienvenut W.V., Lilla S., von Kriegsheim A., Lempens A., Kolch W.
Submitted (DEC-2008) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 2-22 AND 66-86, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT SER-2, IDENTIFICATION BY MASS SPECTROMETRY.
Tissue: Ovarian carcinoma.
[7]"Purified U7 snRNPs lack the Sm proteins D1 and D2 but contain Lsm10, a new 14 kDa Sm D1-like protein."
Pillai R.S., Will C.L., Luehrmann R., Schuemperli D., Mueller B.
EMBO J. 20:5470-5479(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE U7 SNRNP COMPLEX.
[8]"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 SPLICEOSOMAL C COMPLEX.
[9]"The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome."
Will C.L., Schneider C., Hossbach M., Urlaub H., Rauhut R., Elbashir S., Tuschl T., Luehrmann R.
RNA 10:929-941(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN A COMPLEX WITH THE U11/U12 SPLICEOSOME, IDENTIFICATION BY MASS SPECTROMETRY.
[10]"An assembly chaperone collaborates with the SMN complex to generate spliceosomal SnRNPs."
Chari A., Golas M.M., Klingenhager M., Neuenkirchen N., Sander B., Englbrecht C., Sickmann A., Stark H., Fischer U.
Cell 135:497-509(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN SNRNP BIOGENESIS, IDENTIFICATION IN 6S PICLN-SM COMPLEX, IDENTIFICATION IN SMN-SM COMPLEX, SUBCELLULAR LOCATION.
[11]"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].
[12]"Crystal structure of human spliceosomal U1 snRNP at 5.5 A resolution."
Pomeranz Krummel D.A., Oubridge C., Leung A.K., Li J., Nagai K.
Nature 458:475-480(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (5.49 ANGSTROMS) IN SPLICEOSOMAL U1 SNRNP.
[13]"Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis."
Leung A.K., Nagai K., Li J.
Nature 473:536-539(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.60 ANGSTROMS) IN SPLICEOSOMAL CORE U4 SNRNP.
[14]"Structural basis of assembly chaperone-mediated snRNP formation."
Grimm C., Chari A., Pelz J.P., Kuper J., Kisker C., Diederichs K., Stark H., Schindelin H., Fischer U.
Mol. Cell 49:692-703(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN 6S PICLN-SM COMPLEX, IDENTIFICATION IN 6S PICLN-SM COMPLEX, FUNCTION IN CORE U1 SNRNP BIOGENESIS.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS9055.1.
PIRS55053.
RefSeqNP_003086.1. NM_003095.2.
UniGeneHs.105465.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1VU2X-ray3.10D/L/T/b/j/r/z1-86[»]
1VU3X-ray3.10D/L/T/b/j/r1-86[»]
2Y9AX-ray3.60F/M/T1-86[»]
2Y9BX-ray3.60F/M/T1-86[»]
2Y9CX-ray3.60F/M/T1-86[»]
2Y9DX-ray3.60F/M/T1-86[»]
3CW1X-ray5.491/2/F/Z1-86[»]
3PGWX-ray4.40F/I1-86[»]
3S6NX-ray2.50F1-86[»]
4F77X-ray3.10D/L/T/b/j/r/z1-86[»]
4F7UX-ray1.90F/I1-86[»]
ProteinModelPortalP62306.
SMRP62306. Positions 3-76.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112520. 65 interactions.
DIPDIP-31221N.
IntActP62306. 27 interactions.
MINTMINT-1137229.
STRING9606.ENSP00000266735.

PTM databases

PhosphoSiteP62306.

Polymorphism databases

DMDM61237391.

Proteomic databases

MaxQBP62306.
PaxDbP62306.
PeptideAtlasP62306.
PRIDEP62306.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000266735; ENSP00000266735; ENSG00000139343.
GeneID6636.
KEGGhsa:6636.
UCSCuc001tej.3. human.

Organism-specific databases

CTD6636.
GeneCardsGC12P096252.
HGNCHGNC:11162. SNRPF.
MIM603541. gene.
neXtProtNX_P62306.
PharmGKBPA36003.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1958.
HOVERGENHBG052369.
InParanoidP62306.
KOK11098.
OMASTDGYMN.
OrthoDBEOG7HXCTK.
PhylomeDBP62306.
TreeFamTF314481.

Enzyme and pathway databases

ReactomeREACT_1788. Transcription.
REACT_21257. Metabolism of RNA.
REACT_71. Gene Expression.
REACT_78. Post-Elongation Processing of the Transcript.

Gene expression databases

ArrayExpressP62306.
BgeeP62306.
CleanExHS_SNRPF.
GenevestigatorP62306.

Family and domain databases

InterProIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
IPR016487. snRNP_SmF.
[Graphical view]
PfamPF01423. LSM. 1 hit.
[Graphical view]
PIRSFPIRSF006609. snRNP_SmF. 1 hit.
SMARTSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMSSF50182. SSF50182. 1 hit.
ProtoNetSearch...

Other

ChiTaRSSNRPF. human.
EvolutionaryTraceP62306.
GeneWikiSmall_nuclear_ribonucleoprotein_polypeptide_F.
GenomeRNAi6636.
NextBio25853.
PMAP-CutDBP62306.
PROP62306.
SOURCESearch...

Entry information

Entry nameRUXF_HUMAN
AccessionPrimary (citable) accession number: P62306
Secondary accession number(s): A2VCR2 expand/collapse secondary AC list , B2R498, Q15356, Q6IBQ1, Q6P4I0
Entry history
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: July 9, 2014
This is version 102 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

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

Human chromosome 12

Human chromosome 12: entries, gene names and cross-references to MIM