› 4c8q

X-ray diffraction
3.7Å resolution

Crystal structure of the yeast Lsm1-7-Pat1 complex

Released:
DOI: 10.2210/pdb4c8q/pdb
PDB entry 4c8q coloured by chain, front view.
PDB entry 4c8q coloured by chain, side view.
PDB entry 4c8q coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Architecture of the Lsm1-7-Pat1 complex: a conserved assembly in eukaryotic mRNA turnover.
Sharif H, Conti E
Cell Rep 5 283-91 (2013)
PMID: 24139796

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150533 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (8 distinct):
Sm-like protein LSm1 Chain: A
Molecule details ›
Chain: A
Length: 101 amino acids
Theoretical weight: 11.94 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P47017 (Residues: 45-145; Coverage: 59%)
Gene names: J0714, LSM1, SPB8, YJL124C
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm2 Chain: B
Molecule details ›
Chain: B
Length: 105 amino acids
Theoretical weight: 12.22 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P38203 (Residues: 2-95; Coverage: 99%)
Gene names: LSM2, SMX5, SNP3, YBL026W, YBL0425
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm3 Chain: C
Molecule details ›
Chain: C
Length: 89 amino acids
Theoretical weight: 10.04 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P57743 (Residues: 1-89; Coverage: 100%)
Gene names: LSM3, SMX4, USS2, YLR438C-A
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm4 Chain: D
Molecule details ›
Chain: D
Length: 114 amino acids
Theoretical weight: 13.04 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P40070 (Residues: 1-114; Coverage: 61%)
Gene names: LSM4, SDB23, USS1, YER112W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm5 Chain: E
Molecule details ›
Chain: E
Length: 93 amino acids
Theoretical weight: 10.43 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P40089 (Residues: 1-93; Coverage: 100%)
Gene names: LSM5, YER146W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm6 Chain: F
Molecule details ›
Chain: F
Length: 86 amino acids
Theoretical weight: 9.41 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q06406 (Residues: 1-86; Coverage: 100%)
Gene names: D9481.18, LSM6, YDR378C
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm7 Chain: G
Molecule details ›
Chain: G
Length: 115 amino acids
Theoretical weight: 13.03 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P53905 (Residues: 1-115; Coverage: 100%)
Gene names: LSM7, N1202, N1780, YNL147W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Deadenylation-dependent mRNA-decapping factor PAT1 Chain: H
Molecule details ›
Chain: H
Length: 328 amino acids
Theoretical weight: 37.93 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P25644 (Residues: 456-783; Coverage: 41%)
Gene names: MRT1, PAT1, YCR077C, YCR77C
Sequence domains: Topoisomerase II-associated protein PAT1

Ligands and Environments

1 bound ligand:
Ligand CO 2 x CO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P63
Unit cell:
a: 258.687Å b: 258.687Å c: 47.103Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.251 0.249 0.295
Expression system: Escherichia coli

Quick links

Citations

16 review citations

Cellular consequences of arginine methylation.
Lorton et al. (2019)
15 more

2 mentions without citation

The role of disordered protein regions in the assembly of decapping complexes and RNP granules.
Jonas et al. (2013)
1 more