› 4c92

X-ray diffraction
2.3Å resolution

Crystal structure of the yeast Lsm1-7 complex

Released:
DOI: 10.2210/pdb4c92/pdb
PDB entry 4c92 coloured by chain, front view.
PDB entry 4c92 coloured by chain, side view.
PDB entry 4c92 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
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 heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153576 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (7 distinct):
Sm-like protein LSm1 Chain: A
Molecule details ›
Chain: A
Length: 146 amino acids
Theoretical weight: 17.29 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P47017 (Residues: 27-172; Coverage: 85%)
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
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
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
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
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
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
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.

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 61.796Å b: 90.57Å c: 68.462Å
α: 90° β: 100.8° γ: 90°
R-values:
R R work R free
0.213 0.211 0.258
Expression system: Escherichia coli

Quick links

Citations

15 review citations

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

5 mentions without citation

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