› 6ppv

X-ray diffraction
2.05Å resolution

Structure of S. pombe Lsm1-7 with RNA, polyuridine with 3' guanosine

Released:
DOI: 10.2210/pdb6ppv/pdb
PDB entry 6ppv coloured by chain, front view.
PDB entry 6ppv coloured by chain, side view.
PDB entry 6ppv coloured by chain, top view.
Source organism: Schizosaccharomyces pombe 972h-
Primary publication:
Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes.
Montemayor EJ, Virta JM, Hayes SM, Nomura Y, Brow DA, Butcher SE
RNA 26 1400-1413 (2020)
PMID: 32518066

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-126964 (preferred)
Entry contents:
7 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (8 distinct):
U6 snRNA-associated Sm-like protein LSm1 Chain: A
Molecule details ›
Chain: A
Length: 86 amino acids
Theoretical weight: 9.75 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: P87173 (Residues: 1-84; Coverage: 60%)
Gene names: SPBC3D6.08c, lsm1
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm2 Chain: B
Molecule details ›
Chain: B
Length: 96 amino acids
Theoretical weight: 11 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: O94408 (Residues: 1-96; Coverage: 100%)
Gene names: SPCC1620.01c, lsm2
Sequence domains: LSM domain
Probable U6 snRNA-associated Sm-like protein LSm3 Chain: C
Molecule details ›
Chain: C
Length: 95 amino acids
Theoretical weight: 10.82 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y7M4 (Residues: 1-93; Coverage: 100%)
Gene names: SPBC9B6.05c, lsm3
Sequence domains: LSM domain
Probable U6 snRNA-associated Sm-like protein LSm4 Chain: D
Molecule details ›
Chain: D
Length: 129 amino acids
Theoretical weight: 15.01 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: O14352 (Residues: 1-121; Coverage: 100%)
Gene names: SPBC30D10.06, lsm4
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm5 Chain: E
Molecule details ›
Chain: E
Length: 80 amino acids
Theoretical weight: 8.86 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: O42978 (Residues: 1-80; Coverage: 100%)
Gene names: SPBC20F10.09, lsm5
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm6 Chain: F
Molecule details ›
Chain: F
Length: 77 amino acids
Theoretical weight: 8.49 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UUI1 (Residues: 1-75; Coverage: 100%)
Gene names: SPAC2F3.17c, lsm6
Sequence domains: LSM domain
U6 snRNA-associated Sm-like protein LSm7 Chain: G
Molecule details ›
Chain: G
Length: 113 amino acids
Theoretical weight: 12.49 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: O74499 (Residues: 1-113; Coverage: 100%)
Gene names: SPCC285.12, lsm7
Sequence domains: LSM domain
RNA (5'-R(*AP*UP*UP*UP*UP*G)-3') Chain: H
Molecule details ›
Chain: H
Length: 6 nucleotides
Theoretical weight: 1.85 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P3121
Unit cell:
a: 69.023Å b: 69.023Å c: 296.068Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.21 0.209 0.245
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression.
Passmore et al. (2022)
3 more

1 mention without citation

Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes.
Montemayor et al. (2020)