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Protein

Small nuclear ribonucleoprotein Sm D3

Gene

SMD3

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Involved in pre-mRNA splicing. Binds snRNA U1, U2, U4 and U5 which contain a highly conserved structural motif called the Sm binding site. Also binds telomerase RNA and is required for its accumulation.2 Publications

GO - Molecular functioni

  • mRNA binding Source: SGD

GO - Biological processi

  • mRNA splicing, via spliceosome Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-32283-MONOMER.
ReactomeiR-SCE-72165. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Small nuclear ribonucleoprotein Sm D3
Short name:
Sm-D3
Alternative name(s):
snRNP core protein D3
Gene namesi
Name:SMD3
Ordered Locus Names:YLR147C
ORF Names:L9634.6
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XII

Organism-specific databases

EuPathDBiFungiDB:YLR147C.
SGDiS000004137. SMD3.

Subcellular locationi

  • Cytoplasm 1 Publication
  • Nucleus 1 Publication

GO - Cellular componenti

  • commitment complex Source: SGD
  • cytoplasm Source: UniProtKB-SubCell
  • U1 snRNP Source: SGD
  • U2-type prespliceosome Source: SGD
  • U4/U6 x U5 tri-snRNP complex Source: SGD
  • U5 snRNP Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 101101Small nuclear ribonucleoprotein Sm D3PRO_0000122220Add
BLAST

Proteomic databases

MaxQBiP43321.
TopDownProteomicsiP43321.

Interactioni

Subunit structurei

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. SMD3 specifically interacts with SMB1. Belongs to the CWC complex (or CEF1-associated complex), a spliceosome sub-complex reminiscent of a late-stage spliceosome composed of the U2, U5 and U6 snRNAs and at least BUD13, BUD31, BRR2, CDC40, CEF1, CLF1, CUS1, CWC2, CWC15, CWC21, CWC22, CWC23, CWC24, CWC25, CWC27, ECM2, HSH155, IST3, ISY1, LEA1, MSL1, NTC20, PRP8, PRP9, PRP11, PRP19, PRP21, PRP22, PRP45, PRP46, SLU7, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, SNT309, SNU114, SPP2, SYF1, SYF2, RSE1 and YJU2. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1.4 Publications

Protein-protein interaction databases

BioGridi31416. 62 interactions.
DIPiDIP-715N.
IntActiP43321. 25 interactions.
MINTiMINT-517864.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80J/R1-101[»]
5GAMelectron microscopy3.70d1-101[»]
5GANelectron microscopy3.60d/n1-101[»]
5GAOelectron microscopy3.60n1-101[»]
ProteinModelPortaliP43321.
SMRiP43321. Positions 8-84.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP core protein family.Curated

Phylogenomic databases

GeneTreeiENSGT00610000086153.
HOGENOMiHOG000182712.
InParanoidiP43321.
KOiK11088.
OMAiNCQLAET.
OrthoDBiEOG7HTHWG.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PANTHERiPTHR23338. PTHR23338. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

P43321-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTMNGIPVKL LNEAQGHIVS LELTTGATYR GKLVESEDSM NVQLRDVIAT
60 70 80 90 100
EPQGAVTHMD QIFVRGSQIK FIVVPDLLKN APLFKKNSSR PMPPIRGPKR

R
Length:101
Mass (Da):11,224
Last modified:November 1, 1995 - v1
Checksum:iBB02A56C5AD70CF2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti88 – 881S → P in AAS56859 (PubMed:17322287).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M65144 Genomic DNA. No translation available.
Z73319 Genomic DNA. Translation: CAA97719.1.
U53879 Genomic DNA. Translation: AAB82381.1.
AY558533 Genomic DNA. Translation: AAS56859.1.
BK006945 Genomic DNA. Translation: DAA09458.1.
PIRiS29093.
RefSeqiNP_013248.1. NM_001182034.1.

Genome annotation databases

EnsemblFungiiYLR147C; YLR147C; YLR147C.
GeneIDi850839.
KEGGisce:YLR147C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M65144 Genomic DNA. No translation available.
Z73319 Genomic DNA. Translation: CAA97719.1.
U53879 Genomic DNA. Translation: AAB82381.1.
AY558533 Genomic DNA. Translation: AAS56859.1.
BK006945 Genomic DNA. Translation: DAA09458.1.
PIRiS29093.
RefSeqiNP_013248.1. NM_001182034.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80J/R1-101[»]
5GAMelectron microscopy3.70d1-101[»]
5GANelectron microscopy3.60d/n1-101[»]
5GAOelectron microscopy3.60n1-101[»]
ProteinModelPortaliP43321.
SMRiP43321. Positions 8-84.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31416. 62 interactions.
DIPiDIP-715N.
IntActiP43321. 25 interactions.
MINTiMINT-517864.

Proteomic databases

MaxQBiP43321.
TopDownProteomicsiP43321.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYLR147C; YLR147C; YLR147C.
GeneIDi850839.
KEGGisce:YLR147C.

Organism-specific databases

EuPathDBiFungiDB:YLR147C.
SGDiS000004137. SMD3.

Phylogenomic databases

GeneTreeiENSGT00610000086153.
HOGENOMiHOG000182712.
InParanoidiP43321.
KOiK11088.
OMAiNCQLAET.
OrthoDBiEOG7HTHWG.

Enzyme and pathway databases

BioCyciYEAST:G3O-32283-MONOMER.
ReactomeiR-SCE-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

PROiP43321.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PANTHERiPTHR23338. PTHR23338. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Isolation and characterization of PEP3, a gene required for vacuolar biogenesis in Saccharomyces cerevisiae."
    Preston R., Manolson M.F., Becherer K., Weindnhammer E., Kirkpatrick D., Wright R., Jones E.W.
    Mol. Cell. Biol. 11:5801-5812(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "A putative zinc finger protein, Saccharomyces cerevisiae Vps18p, affects late Golgi functions required for vacuolar protein sorting and efficient alpha-factor prohormone maturation."
    Robinson J.S., Graham T.R., Emr S.D.
    Mol. Cell. Biol. 11:5813-5824(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INTERACTION WITH SMB1.
  4. "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] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], RNA-BINDING.
  5. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XII."
    Johnston M., Hillier L.W., Riles L., Albermann K., Andre B., Ansorge W., Benes V., Brueckner M., Delius H., Dubois E., Duesterhoeft A., Entian K.-D., Floeth M., Goffeau A., Hebling U., Heumann K., Heuss-Neitzel D., Hilbert H.
    , Hilger F., Kleine K., Koetter P., Louis E.J., Messenguy F., Mewes H.-W., Miosga T., Moestl D., Mueller-Auer S., Nentwich U., Obermaier B., Piravandi E., Pohl T.M., Portetelle D., Purnelle B., Rechmann S., Rieger M., Rinke M., Rose M., Scharfe M., Scherens B., Scholler P., Schwager C., Schwarz S., Underwood A.P., Urrestarazu L.A., Vandenbol M., Verhasselt P., Vierendeels F., Voet M., Volckaert G., Voss H., Wambutt R., Wedler E., Wedler H., Zimmermann F.K., Zollner A., Hani J., Hoheisel J.D.
    Nature 387:87-90(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  6. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  7. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  8. "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] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE.
  9. "cDNA cloning of the Sm proteins D2 and D3 from human small nuclear ribonucleoproteins: evidence for a direct D1-D2 interaction."
    Lehmeier T., Raker V., Hermann H., Luehrmann R.
    Proc. Natl. Acad. Sci. U.S.A. 91:12317-12321(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  10. "Structurally related but functionally distinct yeast Sm D core small nuclear ribonucleoprotein particle proteins."
    Roy J., Zheng B., Rymond B.C., Woolford J.L. Jr.
    Mol. Cell. Biol. 15:445-455(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION, FUNCTION, SUBCELLULAR LOCATION.
  11. "Identification by mass spectrometry and functional analysis of novel proteins of the yeast [U4/U6.U5] tri-snRNP."
    Gottschalk A., Neubauer G., Banroques J., Mann M., Luehrmann R., Fabrizio P.
    EMBO J. 18:4535-4548(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBUNIT, IDENTIFICATION IN THE U4/U5/U6 TRI-SNRNP COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.
  12. "Saccharomyces cerevisiae telomerase is an Sm small nuclear ribonucleoprotein particle."
    Seto A.G., Zaug A.J., Sobel S.G., Wolin S.L., Cech T.R.
    Nature 401:177-180(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  13. "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] [Europe PMC] [Abstract]
    Cited for: SUBUNIT.
  14. "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] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION OF THE SPLICEOSOME.
  15. "Proteomics analysis reveals stable multiprotein complexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA splicing factors, and snRNAs."
    Ohi M.D., Link A.J., Ren L., Jennings J.L., McDonald W.H., Gould K.L.
    Mol. Cell. Biol. 22:2011-2024(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE CWC COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY.

Entry informationi

Entry nameiSMD3_YEAST
AccessioniPrimary (citable) accession number: P43321
Secondary accession number(s): D6VYE2, E9P8W3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: June 8, 2016
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XII
    Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names

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.