› 6aso

X-ray diffraction
2.71Å resolution

Structure of yeast U6 snRNP with 3'-phosphate terminated U6 RNA

Released:
DOI: 10.2210/pdb6aso/pdb
PDB entry 6aso coloured by chain, front view.
PDB entry 6aso coloured by chain, side view.
PDB entry 6aso coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
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)
PDBe Complex ID:
PDB-CPX-108194 (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: 424 amino acids
Theoretical weight: 49.05 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P49960 (Residues: 28-444; Coverage: 94%)
Gene names: PRP24, YM8156.10C, YMR268C
Sequence domains:
U6 snRNA-associated Sm-like protein LSm2 Chain: B
Molecule details ›
Chain: B
Length: 95 amino acids
Theoretical weight: 11.18 KDa
Source organism: Saccharomyces cerevisiae
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: 97 amino acids
Theoretical weight: 11.08 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: 93 amino acids
Theoretical weight: 10.63 KDa
Source organism: Saccharomyces cerevisiae
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: 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: 88 amino acids
Theoretical weight: 9.55 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: A6ZYX7 (Residues: 1-86; Coverage: 100%)
Gene names: LSM6, SCY_1265
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.
U6 snRNA-associated Sm-like protein LSm8 Chain: H
Molecule details ›
Chain: H
Length: 115 amino acids
Theoretical weight: 13.23 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P47093 (Residues: 1-109; Coverage: 100%)
Gene names: J1464, LSM8, YJR022W, YJR83.16
Sequence domains: LSM domain
Saccharomyces cerevisiae strain HB_S_GIMBLETTROAD_9 chromosome XII sequence Chain: I
Molecule details ›
Chain: I
Length: 84 nucleotides
Theoretical weight: 27.02 KDa
Sequence domains: U6 spliceosomal RNA

Ligands and Environments

3 bound ligands:
Ligand K 2 x K
Ligand MN 1 x MN
Ligand MG 2 x MG
1 modified residue:
Ligand UBD 1 x UBD

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P21
Unit cell:
a: 94.197Å b: 77.39Å c: 118.614Å
α: 90° β: 105.91° γ: 90°
R-values:
R R work R free
0.199 0.195 0.247
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)