› 5mps

Electron Microscopy
3.85Å resolution

Structure of a spliceosome remodeled for exon ligation

Released:
DOI: 10.2210/pdb5mps/pdb
PDB entry 5mps coloured by chain, front view.
PDB entry 5mps coloured by chain, side view.
PDB entry 5mps coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of a spliceosome remodelled for exon ligation.
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K
OpenAccess logo Nature 542 377-380 (2017)
PMID: 28076345
Related structures: EMD-3539

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 30-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-294154 (preferred)
Entry contents:
25 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (30 distinct):
Pre-mRNA-splicing factor 8 Chain: A
Molecule details ›
Chain: A
Length: 2413 amino acids
Theoretical weight: 279.87 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33334 (Residues: 1-2413; Coverage: 100%)
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: 114.17 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36048 (Residues: 1-1008; Coverage: 100%)
Gene names: GIN10, SNU114, YKL173W, YKL637
Sequence domains:
Pre-mRNA-splicing factor CWC22 Chain: H
Pre-mRNA-splicing factor PRP46 Chain: J
Pre-mRNA-processing protein 45 Chain: K
Pre-mRNA-splicing factor BUD31 Chain: L
Pre-mRNA-splicing factor CWC2 Chain: M
Pre-mRNA-splicing factor SLT11 Chain: N
Pre-mRNA-splicing factor CEF1 Chain: O
Pre-mRNA-splicing factor CWC15 Chain: P
Pre-mRNA-splicing factor CWC21 Chain: R
Pre-mRNA-splicing factor CLF1 Chain: S
Pre-mRNA-splicing factor SYF1 Chain: T
Pre-mRNA-splicing factor 18 Chain: a
Pre-mRNA-splicing factor SLU7 Chain: c
Pre-mRNA-processing factor 17 Chain: o
Unknown Chain: X
Pre-mRNA-splicing factor SYF2 Chain: y
Small nuclear ribonucleoprotein-associated protein B Chain: b
Small nuclear ribonucleoprotein Sm D3 Chain: d
Small nuclear ribonucleoprotein E Chain: e
Small nuclear ribonucleoprotein F Chain: f
Small nuclear ribonucleoprotein G Chain: g
Small nuclear ribonucleoprotein Sm D1 Chain: h
Small nuclear ribonucleoprotein Sm D2 Chain: j
Yeast UBC4 gene for ubiquitin-conjugating enzyme Chain: I
UBC4 gene exon Chain: E
U2 snRNA Chain: 2
Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence Chain: 6
U5 snRNA Chain: 5

Ligands and Environments

5 bound ligands:
Ligand MG 3 x MG
Ligand K 2 x K
Ligand IHP 1 x IHP
Ligand GTP 1 x GTP
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.85Å
Relevant EMDB volumes: EMD-3539

Quick links

Citations

28 review citations

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

6 mentions without citation

Structural Basis of Nuclear pre-mRNA Splicing: Lessons from Yeast.
Plaschka et al. (2019)
5 more