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Protein

U6 snRNA-associated Sm-like protein LSm8

Gene

LSM8

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

Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, spliceosomal U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved in degradation of nuclear pre-mRNA by targeting them for decapping. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.4 Publications

GO - Molecular functioni

GO - Biological processi

  • mRNA splicing, via spliceosome Source: SGD
  • rRNA processing Source: UniProtKB-KW
  • tRNA processing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing, rRNA processing, tRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-31662-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm8
Gene namesi
Name:LSM8
Ordered Locus Names:YJR022W
ORF Names:J1464, YJR83.16
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome X

Organism-specific databases

EuPathDBiFungiDB:YJR022W.
SGDiS000003783. LSM8.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-SubCell
  • nucleolus Source: SGD
  • nucleus Source: SGD
  • spliceosomal complex Source: UniProtKB-KW
  • U4/U6 x U5 tri-snRNP complex Source: SGD
  • U6 snRNP Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi57R → A: Reduces affinity for poly-U RNA ends. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002030881 – 109U6 snRNA-associated Sm-like protein LSm8Add BLAST109

Proteomic databases

MaxQBiP47093.
PRIDEiP47093.

Interactioni

Subunit structurei

Component of the heptameric LSM2-LSM8 complex that forms a seven-membered ring structure with a doughnut shape; an RNA strand can pass through the hole in the center of the ring structure. The LSm subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. LSM2-LSM8 associates with PAT1 and XRN1. 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

Binary interactionsi

WithEntry#Exp.IntActNotes
HSH49Q991813EBI-313,EBI-8579
LSM2P382035EBI-313,EBI-180
LSM4P400703EBI-313,EBI-188
LSM6Q064064EBI-313,EBI-196
PRP24P499603EBI-313,EBI-212
PRP4P200533EBI-313,EBI-219

Protein-protein interaction databases

BioGridi33776. 85 interactors.
DIPiDIP-903N.
IntActiP47093. 64 interactors.
MINTiMINT-383498.

Structurei

Secondary structure

1109
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 8Combined sources3
Beta strandi11 – 17Combined sources7
Beta strandi22 – 30Combined sources9
Beta strandi36 – 43Combined sources8
Turni44 – 47Combined sources4
Beta strandi48 – 56Combined sources9
Helixi58 – 60Combined sources3
Beta strandi61 – 66Combined sources6
Helixi96 – 102Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80b1-109[»]
4M77X-ray3.11A/H1-109[»]
4M78X-ray2.79A/H1-96[»]
4M7AX-ray2.78A/H1-96[»]
4M7DX-ray2.60A/H1-96[»]
5GANelectron microscopy3.6081-109[»]
ProteinModelPortaliP47093.
SMRiP47093.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

HOGENOMiHOG000000816.
InParanoidiP47093.
KOiK12627.
OrthoDBiEOG092C5VL3.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

P47093-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSATLKDYLN KRVVIIKVDG ECLIASLNGF DKNTNLFITN VFNRISKEFI
60 70 80 90 100
CKAQLLRGSE IALVGLIDAE NDDSLAPIDE KKVPMLKDTK NKIENEHVIW

EKVYESKTK
Length:109
Mass (Da):12,385
Last modified:October 3, 2006 - v2
Checksum:iB6E37F585B6292EA
GO

Sequence cautioni

The sequence CAA60945 differs from that shown. Reason: Erroneous initiation.Curated
The sequence CAA89547 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X87611 Genomic DNA. Translation: CAA60945.1. Different initiation.
Z49522 Genomic DNA. Translation: CAA89547.1. Different initiation.
X87297 Genomic DNA. No translation available.
BK006943 Genomic DNA. Translation: DAA08812.1.
PIRiS55211.
RefSeqiNP_012556.2. NM_001181680.1.

Genome annotation databases

EnsemblFungiiYJR022W; YJR022W; YJR022W.
GeneIDi853479.
KEGGisce:YJR022W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X87611 Genomic DNA. Translation: CAA60945.1. Different initiation.
Z49522 Genomic DNA. Translation: CAA89547.1. Different initiation.
X87297 Genomic DNA. No translation available.
BK006943 Genomic DNA. Translation: DAA08812.1.
PIRiS55211.
RefSeqiNP_012556.2. NM_001181680.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCMelectron microscopy3.80b1-109[»]
4M77X-ray3.11A/H1-109[»]
4M78X-ray2.79A/H1-96[»]
4M7AX-ray2.78A/H1-96[»]
4M7DX-ray2.60A/H1-96[»]
5GANelectron microscopy3.6081-109[»]
ProteinModelPortaliP47093.
SMRiP47093.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33776. 85 interactors.
DIPiDIP-903N.
IntActiP47093. 64 interactors.
MINTiMINT-383498.

Proteomic databases

MaxQBiP47093.
PRIDEiP47093.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYJR022W; YJR022W; YJR022W.
GeneIDi853479.
KEGGisce:YJR022W.

Organism-specific databases

EuPathDBiFungiDB:YJR022W.
SGDiS000003783. LSM8.

Phylogenomic databases

HOGENOMiHOG000000816.
InParanoidiP47093.
KOiK12627.
OrthoDBiEOG092C5VL3.

Enzyme and pathway databases

BioCyciYEAST:G3O-31662-MONOMER.

Miscellaneous databases

PROiP47093.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. LSM_dom_euk/arc.
[Graphical view]
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiLSM8_YEAST
AccessioniPrimary (citable) accession number: P47093
Secondary accession number(s): D6VWJ6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: October 3, 2006
Last modified: November 2, 2016
This is version 131 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1440 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, 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 X
    Yeast (Saccharomyces cerevisiae) chromosome X: 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.