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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: 5 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

Keywordsi

Molecular functionRibonucleoprotein, RNA-binding
Biological processmRNA processing, mRNA splicing

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

GO - Cellular componenti

  • catalytic step 2 spliceosome Source: GO_Central
  • commitment complex Source: SGD
  • pICln-Sm protein complex Source: GO_Central
  • precatalytic spliceosome Source: GO_Central
  • SMN-Sm protein complex Source: GO_Central
  • U12-type spliceosomal complex Source: GO_Central
  • U1 snRNP Source: SGD
  • U2 snRNP Source: GO_Central
  • U2-type prespliceosome Source: SGD
  • U4/U6 x U5 tri-snRNP complex Source: SGD
  • U4 snRNP Source: GO_Central
  • U5 snRNP Source: SGD

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001222201 – 101Small nuclear ribonucleoprotein Sm D3Add BLAST101

Proteomic databases

MaxQBiP43321.
PRIDEiP43321.
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. 63 interactors.
DIPiDIP-715N.
IntActiP43321. 25 interactors.
MINTiMINT-517864.

Structurei

Secondary structure

1101
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 14Combined sources9
Beta strandi17 – 25Combined sources9
Beta strandi29 – 35Combined sources7
Beta strandi42 – 50Combined sources9
Beta strandi52 – 54Combined sources3
Beta strandi56 – 64Combined sources9
Helixi66 – 68Combined sources3
Beta strandi69 – 74Combined sources6
Helixi76 – 79Combined sources4
Beta strandi81 – 83Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80J/R1-101[»]
5GAMelectron microscopy3.70d1-101[»]
5GANelectron microscopy3.60d/n1-101[»]
5GAOelectron microscopy3.60n1-101[»]
5GM6electron microscopy3.50l1-101[»]
5GMKelectron microscopy3.40l/y1-101[»]
5LJ3electron microscopy3.80d/n1-101[»]
5LJ5electron microscopy3.80d/n1-101[»]
5LQWelectron microscopy5.80d1-101[»]
ProteinModelPortaliP43321.
SMRiP43321.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP core protein family.Curated

Phylogenomic databases

GeneTreeiENSGT00610000086153.
HOGENOMiHOG000182712.
InParanoidiP43321.
KOiK11088.
OMAiNCQLAET.
OrthoDBiEOG09265LYI.

Family and domain databases

CDDicd01721. Sm_D3. 1 hit.
InterProiView protein in InterPro
IPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
IPR034099. SmD3.
PANTHERiPTHR23338. PTHR23338. 1 hit.
PfamiView protein in Pfam
PF01423. LSM. 1 hit.
SMARTiView protein in SMART
SM00651. Sm. 1 hit.
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)DescriptionActionsGraphical viewLength
Sequence conflicti88S → P in AAS56859 (PubMed:17322287).Curated1

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80J/R1-101[»]
5GAMelectron microscopy3.70d1-101[»]
5GANelectron microscopy3.60d/n1-101[»]
5GAOelectron microscopy3.60n1-101[»]
5GM6electron microscopy3.50l1-101[»]
5GMKelectron microscopy3.40l/y1-101[»]
5LJ3electron microscopy3.80d/n1-101[»]
5LJ5electron microscopy3.80d/n1-101[»]
5LQWelectron microscopy5.80d1-101[»]
ProteinModelPortaliP43321.
SMRiP43321.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi31416. 63 interactors.
DIPiDIP-715N.
IntActiP43321. 25 interactors.
MINTiMINT-517864.

Proteomic databases

MaxQBiP43321.
PRIDEiP43321.
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.
OrthoDBiEOG09265LYI.

Enzyme and pathway databases

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

Miscellaneous databases

PROiP43321.

Family and domain databases

CDDicd01721. Sm_D3. 1 hit.
InterProiView protein in InterPro
IPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
IPR034099. SmD3.
PANTHERiPTHR23338. PTHR23338. 1 hit.
PfamiView protein in Pfam
PF01423. LSM. 1 hit.
SMARTiView protein in SMART
SM00651. Sm. 1 hit.
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSMD3_YEAST
AccessioniPrimary (citable) accession number: P43321
Secondary accession number(s): D6VYE2, E9P8W3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: February 15, 2017
This is version 135 of the entry and version 1 of the sequence. See 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.