› 4m7a

X-ray diffraction
2.78Å resolution

Crystal structure of Lsm2-8 complex bound to the 3' end sequence of U6 snRNA

Released:
DOI: 10.2210/pdb4m7a/pdb
PDB entry 4m7a coloured by chain, front view.
PDB entry 4m7a coloured by chain, side view.
PDB entry 4m7a coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Crystal structures of the Lsm complex bound to the 3' end sequence of U6 small nuclear RNA.
Zhou L, Hang J, Zhou Y, Wan R, Lu G, Yin P, Yan C, Shi Y
Nature 506 116-20 (2014)
PMID: 24240276

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero octamer (preferred)
hetero hexadecamer
Assembly name:
PDBe Complex ID:
PDB-CPX-153579 (preferred)
Entry contents:
7 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (8 distinct):
U6 snRNA-associated Sm-like protein LSm8 Chains: A, H
Molecule details ›
Chains: A, H
Length: 96 amino acids
Theoretical weight: 10.72 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P47093 (Residues: 1-96; Coverage: 88%)
Gene names: J1464, LSM8, YJR022W, YJR83.16
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm2 Chains: B, I
Molecule details ›
Chains: B, I
Length: 95 amino acids
Theoretical weight: 11.16 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P38203 (Residues: 1-95; Coverage: 100%)
Gene names: LSM2, SMX5, SNP3, YBL026W, YBL0425
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA-associated Sm-like protein LSm3 Chains: C, J
Molecule details ›
Chains: C, J
Length: 89 amino acids
Theoretical weight: 10.01 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 LSm6 Chains: D, K
Molecule details ›
Chains: D, K
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 LSm5 Chains: E, L
Molecule details ›
Chains: E, L
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 LSm7 Chains: F, M
Molecule details ›
Chains: F, M
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.
U6 snRNA-associated Sm-like protein LSm4 Chains: G, N
Molecule details ›
Chains: G, N
Length: 93 amino acids
Theoretical weight: 10.63 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P40070 (Residues: 1-93; Coverage: 50%)
Gene names: LSM4, SDB23, USS1, YER112W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U6 snRNA Chains: O, P
Molecule details ›
Chains: O, P
Length: 8 nucleotides
Theoretical weight: 2.44 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2
Unit cell:
a: 117.624Å b: 78.379Å c: 140.565Å
α: 90° β: 100.58° γ: 90°
R-values:
R R work R free
0.246 0.245 0.278
Expression system: Escherichia coli

Quick links

Citations

15 review citations

Mechanistic insights into precursor messenger RNA splicing by the spliceosome.
Shi Y. (2017)
14 more

4 mentions without citation

An RNA-centric historical narrative around the Protein Data Bank.
Westhof et al. (2021)
3 more