› 5wsg

Electron Microscopy
4Å resolution

Cryo-EM structure of the Catalytic Step II spliceosome (C* complex) at 4.0 angstrom resolution

Released:
DOI: 10.2210/pdb5wsg/pdb
PDB entry 5wsg coloured by chain, front view.
PDB entry 5wsg coloured by chain, side view.
PDB entry 5wsg coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structure of a yeast step II catalytically activated spliceosome.
Yan C, Wan R, Bai R, Huang G, Shi Y
Science 355 149-155 (2017)
PMID: 27980089
Related structures: EMD-6684

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 45-mer (preferred)
PDBe Complex ID:
PDB-CPX-294013 (preferred)
Entry contents:
28 distinct polypeptide molecules
7 distinct RNA molecules
Macromolecules (35 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 S288C
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 S288C
UniProt:
  • Canonical: P36048 (Residues: 1-1008; Coverage: 100%)
Gene names: GIN10, SNU114, YKL173W, YKL637
Sequence domains:
Pre-mRNA-splicing factor CWC21 Chain: J
Pre-mRNA-splicing factor PRP46 Chain: O
Pre-mRNA-processing protein 45 Chain: P
Pre-mRNA-splicing factor SLT11 Chain: Q
Pre-mRNA-splicing factor CWC2 Chain: R
Pre-mRNA-splicing factor CWC15 Chain: S
Pre-mRNA-splicing factor BUD31 Chain: T
Pre-mRNA-splicing factor CWC22 Chain: Z
Pre-mRNA-splicing factor CEF1 Chain: c
Pre-mRNA-splicing factor CLF1 Chain: d
Pre-mRNA-splicing factor SYF2 Chain: I
Pre-mRNA-splicing factor SYF1 Chain: v
Pre-mRNA-processing factor 17 Chain: n
Pre-mRNA-processing factor 19 Chains: o, p, q, r
Pre-mRNA-splicing factor SNT309 Chain: t
Small nuclear ribonucleoprotein-associated protein B Chains: F, k
Small nuclear ribonucleoprotein E Chains: G, i
Small nuclear ribonucleoprotein F Chains: H, h
Small nuclear ribonucleoprotein G Chains: K, j
Small nuclear ribonucleoprotein Sm D3 Chains: U, l
Small nuclear ribonucleoprotein Sm D1 Chains: V, m
Small nuclear ribonucleoprotein Sm D2 Chains: W, g
U2 small nuclear ribonucleoprotein B'' Chain: X
U2 small nuclear ribonucleoprotein A' Chain: Y
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 Chain: e
Pre-mRNA-splicing factor 18 Chain: f
5'-exon Chain: B
5'-intron-lariat Chain: N
U5 snRNA Chain: D
Saccharomyces cerevisiae S288c SNR6 snRNA Chain: E
RNA (91-MER) Chain: L
3'-intron-lariat Chain: M
3'-exon-intron Chain: b

Ligands and Environments

3 bound ligands:
Ligand GTP 1 x GTP
Ligand MG 6 x MG
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 4Å
Relevant EMDB volumes: EMD-6684

Quick links

Citations

27 review citations

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

13 mentions without citation

Molecular Mechanisms of pre-mRNA Splicing through Structural Biology of the Spliceosome.
Yan et al. (2019)
12 more