P54999 (RUXF_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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:	SMX3
Ordered Locus Names:	YPR182W
ORF Names:	P9705.4

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	86 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site.
Subunit structure	Component of the Sm core complex, present in spliceosomal snRNP U1, U2, U4/U6 and U5. The core complex contains SMB1, SMD1, SMD2, SMD3, SME1, SMX3 and SMX2 (Sm proteins B, D1, D2, D3, E, F and G, respectively), and is probably a heptameric ring structure. SMX3 specifically interacts with SME1. Ref.2 Ref.9
Subcellular location	Nucleus.
Miscellaneous	Present with 2570 molecules/cell in log phase SD medium. Ref.10
Sequence similarities	Belongs to the snRNP Sm proteins family. SmF/LSm6 subfamily.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus
Ligand	RNA-binding
Molecular function	Ribonucleoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	nuclear mRNA splicing, via spliceosome Inferred from physical interaction. Source: SGD
Cellular component	U1 snRNP Inferred from direct assay Ref.6. Source: SGD U4/U6 x U5 tri-snRNP complex Inferred from direct assay. Source: SGD U5 snRNP Inferred from direct assay. Source: SGD
Molecular function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
SMD2	Q06217	3	EBI-770,EBI-235
SME1	Q12330	3	EBI-770,EBI-16359

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 86

86

Small nuclear ribonucleoprotein F

PRO_0000125544

Secondary structure

1

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86

Helix Strand Turn

Details...

Helix

20 – 22

3

Beta strand

25 – 33

9

Beta strand

36 – 44

9

Turn

47 – 49

3

Beta strand

51 – 60

10

Beta strand

63 – 67

5

Beta strand

70 – 73

4

Helix

75 – 77

3

Beta strand

78 – 83

6

Sequences

	Sequence		Length	Mass (Da)
	P54999 [UniParc]. Last modified October 1, 1996. Version 1. Checksum: 1640D3237597B2D8	FASTA	86	9,660
	10 20 30 40 50 60 MSESSDISAM QPVNPKPFLK GLVNHRVGVK LKFNSTEYRG TLVSTDNYFN LQLNEAEEFV 70 80 AGVSHGTLGE IFIRCNNVLY IRELPN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sm and Sm-like proteins belong to a large family: identification of proteins of the U6 as well as the U1, U2, U4 and U5 snRNPs." Seraphin B. EMBO J. 14:2089-2099(1995) [PubMed: 7744014] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Interactions within the yeast Sm core complex: from proteins to amino acids." Camasses A., Bragado-Nilsson E., Martin R., Seraphin B., Bordonne R. Mol. Cell. Biol. 18:1956-1966(1998) [PubMed: 9528767] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INTERACTION WITH SME1.
[3]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI." Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M. , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J. Nature 387:103-105(1997) [PubMed: 9169875] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[4]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[5]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[6]	"Identification of the proteins of the yeast U1 small nuclear ribonucleoprotein complex by mass spectrometry." Neubauer G., Gottschalk A., Fabrizio P., Seraphin B., Luehrmann R., Mann M. Proc. Natl. Acad. Sci. U.S.A. 94:385-390(1997) [PubMed: 9012791] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE.
[7]	"Composition and functional characterization of the yeast spliceosomal penta-snRNP." Stevens S.W., Ryan D.E., Ge H.Y., Moore R.E., Young M.K., Lee T.D., Abelson J. Mol. Cell 9:31-44(2002) [PubMed: 11804584] [Abstract] Cited for: CHARACTERIZATION OF THE SPLICEOSOME.
[8]	"Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin." Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B. EMBO J. 18:3451-3462(1999) [PubMed: 10369684] [Abstract] Cited for: RNA-BINDING.
[9]	"Stoichiometry of the Sm proteins in yeast spliceosomal snRNPs supports the heptamer ring model of the core domain." Walke S., Bragado-Nilsson E., Seraphin B., Nagai K. J. Mol. Biol. 308:49-58(2001) [PubMed: 11302706] [Abstract] Cited for: SUBUNIT.
[10]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[11]	"Homomeric ring assemblies of eukaryotic Sm proteins have affinity for both RNA and DNA. Crystal structure of an oligomeric complex of yeast SmF." Collins B.M., Cubeddu L., Naidoo N., Harrop S.J., Kornfeld G.D., Dawes I.W., Curmi P.M., Mabbutt B.C. J. Biol. Chem. 278:17291-17298(2003) [PubMed: 12618433] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF WILD-TYPE AND MUTANT SER-75.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X82778 Genomic DNA. Translation: CAA58022.1.
U25842 Genomic DNA. Translation: AAB68115.1.
AY558049 Genomic DNA. Translation: AAS56375.1.
BK006949 Genomic DNA. Translation: DAA11598.1.

PIR

S55055.

RefSeq

NP_015508.1. NM_001184279.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1N9R	X-ray	2.80	A/B/C/D/E/F/G	1-86	[»]
1N9S	X-ray	3.50	A/B/C/D/E/F/G/H/I/J/K/L/M/N	1-86	[»]

ProteinModelPortal

P54999.

SMR

P54999. Positions 18-86.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1634N.

IntAct

P54999. 44 interactions.

MINT

MINT-391069.

STRING

P54999.

Proteomic databases

PeptideAtlas

P54999.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YPR182W; YPR182W; YPR182W.

GeneID

856312.

KEGG

sce:YPR182W.

NMPDR

fig|4932.3.peg.6657.

Organism-specific databases

CYGD

YPR182w.

SGD

S000006386. SMX3.

Phylogenomic databases

eggNOG

fuNOG11880.

GeneTree

EFGT00050000005241.

HOGENOM

HBG749684.

OMA

STDNYFN.

OrthoDB

EOG4GJ2ZZ.

Gene expression databases

ArrayExpress

P54999.

Genevestigator

P54999.

GermOnline

YPR182W. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR010920. LSM-related_domain.
IPR001163. LSM_domain.
IPR006649. LSM_domain_euk/arc.
IPR016487. snRNP_SmF.
[Graphical view]

KO

K11098.

Pfam

PF01423. LSM. 1 hit.
[Graphical view]

PIRSF

PIRSF006609. snRNP_SmF. 1 hit.

SMART

SM00651. Sm. 1 hit.
[Graphical view]

SUPFAM

SSF50182. Sm_like_riboprot. 1 hit.

ProtoNet

Search...

Other

NextBio

981688.

Entry information

Entry name

RUXF_YEAST

Accession

Primary (citable) accession number: P54999
Secondary accession number(s): D6W4I2

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	October 1, 1996
Last modified:	December 14, 2011
This is version 109 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program