UniProtKB - Q02260 (SMD1_YEAST)
Small nuclear ribonucleoprotein Sm D1
SMD1
Functioni
Miscellaneous
GO - Molecular functioni
- mRNA binding Source: SGD
- RNA binding Source: GO_Central
GO - Biological processi
- mRNA splicing, via spliceosome Source: UniProtKB
- spliceosomal snRNP assembly Source: GO_Central
Keywordsi
Molecular function | Ribonucleoprotein, RNA-binding |
Biological process | mRNA processing, mRNA splicing |
Names & Taxonomyi
Protein namesi | Recommended name: Small nuclear ribonucleoprotein Sm D1Short name: Sm-D1 Alternative name(s): snRNP core protein D1 |
Gene namesi | Name:SMD1 Ordered Locus Names:YGR074W |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
EuPathDBi | FungiDB:YGR074W |
SGDi | S000003306, SMD1 |
Subcellular locationi
Nucleus
Cytosol
- cytosol Source: SGD
Nucleus
- catalytic step 2 spliceosome Source: GO_Central
- commitment complex Source: SGD
- nucleus Source: SGD
- precatalytic spliceosome Source: GO_Central
- small nuclear ribonucleoprotein complex Source: UniProtKB
- spliceosomal tri-snRNP complex Source: GO_Central
- U1 snRNP Source: SGD
- U12-type spliceosomal complex Source: GO_Central
- U2 snRNP Source: GO_Central
- U2-type prespliceosome Source: SGD
- U4 snRNP Source: GO_Central
- U4/U6 x U5 tri-snRNP complex Source: SGD
- U5 snRNP Source: SGD
Other locations
- pICln-Sm protein complex Source: GO_Central
- SMN-Sm protein complex Source: GO_Central
Keywords - Cellular componenti
NucleusPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000122206 | 1 – 146 | Small nuclear ribonucleoprotein Sm D1Add BLAST | 146 |
Proteomic databases
MaxQBi | Q02260 |
PaxDbi | Q02260 |
PRIDEi | Q02260 |
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. 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.
3 PublicationsProtein-protein interaction databases
BioGRIDi | 33316, 382 interactors |
ComplexPortali | CPX-1651, PRP19-associated complex CPX-23, U1 snRNP CPX-25, U4/U6.U5 tri-snRNP complex CPX-26, U2 snRNP CPX-29, U5 snRNP CPX-30, AAR2-U5 snRNP CPX-31, U4 snRNP CPX-32, U4/U6 snRNP CPX-43, Sm complex |
DIPi | DIP-227N |
IntActi | Q02260, 26 interactors |
MINTi | Q02260 |
STRINGi | 4932.YGR074W |
Miscellaneous databases
RNActi | Q02260, protein |
Structurei
Secondary structure
3D structure databases
SMRi | Q02260 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Motif
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Motifi | 128 – 144 | Nuclear localization signalSequence analysisAdd BLAST | 17 |
Domaini
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG3428, Eukaryota |
HOGENOMi | CLU_123956_2_0_1 |
InParanoidi | Q02260 |
OMAi | TVSPQMN |
Family and domain databases
InterProi | View protein in InterPro IPR027141, LSm4/Sm_D1/D3 IPR001163, LSM_dom_euk/arc IPR010920, LSM_dom_sf |
PANTHERi | PTHR23338, PTHR23338, 1 hit |
Pfami | View protein in Pfam PF01423, LSM, 1 hit |
SMARTi | View protein in SMART SM00651, Sm, 1 hit |
SUPFAMi | SSF50182, SSF50182, 1 hit |
i Sequence
Sequence statusi: Complete.
10 20 30 40 50
MKLVNFLKKL RNEQVTIELK NGTTVWGTLQ SVSPQMNAIL TDVKLTLPQP
60 70 80 90 100
RLNKLNSNGI AMASLYLTGG QQPTASDNIA SLQYINIRGN TIRQIILPDS
110 120 130 140
LNLDSLLVDQ KQLNSLRRSG QIANDPSKKR RRDFGAPANK RPRRGL
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L04669 Genomic DNA Translation: AAA35055.1 Z72858 Genomic DNA Translation: CAA97076.1 AY692847 Genomic DNA Translation: AAT92866.1 BK006941 Genomic DNA Translation: DAA08167.1 |
PIRi | A47264 |
RefSeqi | NP_011588.3, NM_001181203.3 |
Genome annotation databases
EnsemblFungii | YGR074W_mRNA; YGR074W; YGR074W |
GeneIDi | 852964 |
KEGGi | sce:YGR074W |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L04669 Genomic DNA Translation: AAA35055.1 Z72858 Genomic DNA Translation: CAA97076.1 AY692847 Genomic DNA Translation: AAT92866.1 BK006941 Genomic DNA Translation: DAA08167.1 |
PIRi | A47264 |
RefSeqi | NP_011588.3, NM_001181203.3 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
3JCM | electron microscopy | 3.80 | P/T | 1-146 | [»] | |
5GAM | electron microscopy | 3.70 | h | 1-146 | [»] | |
5GAN | electron microscopy | 3.60 | h/l | 1-146 | [»] | |
5GAO | electron microscopy | 3.60 | l | 1-146 | [»] | |
5GM6 | electron microscopy | 3.50 | m | 1-146 | [»] | |
5GMK | electron microscopy | 3.40 | m/z | 1-146 | [»] | |
5LJ3 | electron microscopy | 3.80 | h/l | 1-146 | [»] | |
5LJ5 | electron microscopy | 3.80 | h/l | 1-146 | [»] | |
5LQW | electron microscopy | 5.80 | h | 1-146 | [»] | |
5MPS | electron microscopy | 3.85 | h | 1-146 | [»] | |
5MQ0 | electron microscopy | 4.17 | h/l | 1-146 | [»] | |
5NRL | electron microscopy | 7.20 | h/l/t | 1-146 | [»] | |
5WSG | electron microscopy | 4.00 | V/m | 1-146 | [»] | |
5Y88 | electron microscopy | 3.70 | f/m | 1-146 | [»] | |
5YLZ | electron microscopy | 3.60 | f/m | 1-146 | [»] | |
5ZWM | electron microscopy | 3.40 | Q/b/m | 1-146 | [»] | |
5ZWN | electron microscopy | 3.30 | b | 1-146 | [»] | |
5ZWO | electron microscopy | 3.90 | Q/b/m | 1-146 | [»] | |
6BK8 | electron microscopy | 3.30 | h/p | 1-146 | [»] | |
6EXN | electron microscopy | 3.70 | h/l | 1-146 | [»] | |
6G90 | electron microscopy | 4.00 | h/t | 1-146 | [»] | |
6J6G | electron microscopy | 3.20 | m/z | 1-146 | [»] | |
6J6H | electron microscopy | 3.60 | m/z | 1-146 | [»] | |
6J6N | electron microscopy | 3.86 | m/z | 1-146 | [»] | |
6J6Q | electron microscopy | 3.70 | m/z | 1-146 | [»] | |
6N7P | electron microscopy | 3.60 | L | 1-146 | [»] | |
6N7R | electron microscopy | 3.20 | L | 1-146 | [»] | |
6N7X | electron microscopy | 3.60 | L | 1-146 | [»] | |
SMRi | Q02260 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 33316, 382 interactors |
ComplexPortali | CPX-1651, PRP19-associated complex CPX-23, U1 snRNP CPX-25, U4/U6.U5 tri-snRNP complex CPX-26, U2 snRNP CPX-29, U5 snRNP CPX-30, AAR2-U5 snRNP CPX-31, U4 snRNP CPX-32, U4/U6 snRNP CPX-43, Sm complex |
DIPi | DIP-227N |
IntActi | Q02260, 26 interactors |
MINTi | Q02260 |
STRINGi | 4932.YGR074W |
Proteomic databases
MaxQBi | Q02260 |
PaxDbi | Q02260 |
PRIDEi | Q02260 |
Genome annotation databases
EnsemblFungii | YGR074W_mRNA; YGR074W; YGR074W |
GeneIDi | 852964 |
KEGGi | sce:YGR074W |
Organism-specific databases
EuPathDBi | FungiDB:YGR074W |
SGDi | S000003306, SMD1 |
Phylogenomic databases
eggNOGi | KOG3428, Eukaryota |
HOGENOMi | CLU_123956_2_0_1 |
InParanoidi | Q02260 |
OMAi | TVSPQMN |
Miscellaneous databases
PROi | PR:Q02260 |
RNActi | Q02260, protein |
Family and domain databases
InterProi | View protein in InterPro IPR027141, LSm4/Sm_D1/D3 IPR001163, LSM_dom_euk/arc IPR010920, LSM_dom_sf |
PANTHERi | PTHR23338, PTHR23338, 1 hit |
Pfami | View protein in Pfam PF01423, LSM, 1 hit |
SMARTi | View protein in SMART SM00651, Sm, 1 hit |
SUPFAMi | SSF50182, SSF50182, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | SMD1_YEAST | |
Accessioni | Q02260Primary (citable) accession number: Q02260 Secondary accession number(s): D6VUK6 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | October 1, 1993 |
Last sequence update: | October 1, 1993 | |
Last modified: | December 2, 2020 | |
This is version 181 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families - Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Yeast chromosome VII
Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names