5gam

Electron Microscopy
3.7Å resolution

Foot region of the yeast spliceosomal U4/U6.U5 tri-snRNP

Released:
Source organism: Saccharomyces cerevisiae
Related structures: EMD-8011

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152597 (preferred)
Entry contents:
10 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (12 distinct):
Pre-mRNA-splicing factor 8 Chain: A
Molecule details ›
Chain: A
Length: 735 amino acids
Theoretical weight: 85.83 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33334 (Residues: 1-735; Coverage: 31%)
Gene names: DBF3, DNA39, PRP8, RNA8, SLT21, USA2, YHR165C
Sequence domains:
Pre-mRNA-splicing factor SNU114 Chain: C
Molecule details ›
Chain: C
Length: 1008 amino acids
Theoretical weight: 114.13 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36048 (Residues: 1-1008; Coverage: 100%)
Gene names: GIN10, SNU114, YKL173W, YKL637
Sequence domains:
Small nuclear ribonucleoprotein-associated protein B Chain: b
Molecule details ›
Chain: b
Length: 196 amino acids
Theoretical weight: 22.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40018 (Residues: 1-196; Coverage: 100%)
Gene names: SMB1, YER029C
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chain: e
Molecule details ›
Chain: e
Length: 94 amino acids
Theoretical weight: 10.39 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12330 (Residues: 1-94; Coverage: 100%)
Gene names: SME1, YOR159C
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein F Chain: f
Molecule details ›
Chain: f
Length: 86 amino acids
Theoretical weight: 9.67 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P54999 (Residues: 1-86; Coverage: 100%)
Gene names: P9705.4, SMX3, YPR182W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein G Chain: g
Molecule details ›
Chain: g
Length: 77 amino acids
Theoretical weight: 8.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40204 (Residues: 1-77; Coverage: 100%)
Gene names: SMX2, SNP2, YFL017Bw, YFL017W-A
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Unknown polypeptide Chain: x
Molecule details ›
Chain: x
Length: 18 amino acids
Theoretical weight: 1.55 KDa
Source organism: Saccharomyces cerevisiae
Small nuclear ribonucleoprotein Sm D3 Chain: d
Molecule details ›
Chain: d
Length: 101 amino acids
Theoretical weight: 11.24 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P43321 (Residues: 1-101; Coverage: 100%)
Gene names: L9634.6, SMD3, YLR147C
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D1 Chain: h
Molecule details ›
Chain: h
Length: 146 amino acids
Theoretical weight: 16.3 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02260 (Residues: 1-146; Coverage: 100%)
Gene names: SMD1, YGR074W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D2 Chain: j
Molecule details ›
Chain: j
Length: 110 amino acids
Theoretical weight: 12.88 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06217 (Residues: 1-110; Coverage: 100%)
Gene names: L9328.5, SMD2, YLR275W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U5 snRNA Chain: U
Molecule details ›
Chain: U
Length: 178 nucleotides
Theoretical weight: 57.14 KDa
Sequence domains: U5 spliceosomal RNA
U6 snRNA, 5' end Chain: W
Molecule details ›
Chain: W
Length: 31 nucleotides
Theoretical weight: 9.93 KDa

Ligands and Environments

1 bound ligand:
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-8011