› 5vsu

X-ray diffraction
3.1Å resolution

Structure of yeast U6 snRNP with 2'-phosphate terminated U6 RNA

Released:
DOI: 10.2210/pdb5vsu/pdb
PDB entry 5vsu coloured by chain, front view.
PDB entry 5vsu coloured by chain, side view.
PDB entry 5vsu coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA.
Montemayor EJ, Didychuk AL, Yake AD, Sidhu GK, Brow DA, Butcher SE
Nat Commun 9 1749 (2018)
PMID: 29717126

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153577 (preferred)
Entry contents:
8 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (9 distinct):
U4/U6 snRNA-associated-splicing factor PRP24 Chain: A
Molecule details ›
Chain: A
Length: 452 amino acids
Theoretical weight: 52 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P49960 (Residues: 1-444; Coverage: 100%)
Gene names: PRP24, YM8156.10C, YMR268C
Sequence domains:
U6 snRNA-associated Sm-like protein LSm2 Chain: B
Molecule details ›
Chain: B
Length: 98 amino acids
Theoretical weight: 11.45 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 Chain: C
Molecule details ›
Chain: C
Length: 92 amino acids
Theoretical weight: 10.31 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: 96 amino acids
Theoretical weight: 10.9 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-associated Sm-like protein LSm5 Chain: E
Molecule details ›
Chain: E
Length: 96 amino acids
Theoretical weight: 10.71 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: 88 amino acids
Theoretical weight: 9.55 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: 118 amino acids
Theoretical weight: 13.3 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 LSm8 Chain: H
Molecule details ›
Chain: H
Length: 111 amino acids
Theoretical weight: 12.55 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P47093 (Residues: 1-109; Coverage: 100%)
Gene names: J1464, LSM8, YJR022W, YJR83.16
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Saccharomyces cerevisiae strain T8 chromosome XII sequence Chain: I
Molecule details ›
Chain: I
Length: 83 nucleotides
Theoretical weight: 26.7 KDa
Sequence domains: U6 spliceosomal RNA

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 9QV 1 x 9QV

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 70.157Å b: 114.728Å c: 179.844Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.239 0.234 0.298
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Modifications in small nuclear RNAs and their roles in spliceosome assembly and function.
Bohnsack et al. (2018)
1 more

1 mention without citation

Architecture of the U6 snRNP reveals specific recognition of 3'-end processed U6 snRNA.
Montemayor et al. (2018)