› 6exn

Electron Microscopy
3.7Å resolution

Post-catalytic P complex spliceosome with 3' splice site docked

Released:
DOI: 10.2210/pdb6exn/pdb
PDB entry 6exn coloured by chain, front view.
PDB entry 6exn coloured by chain, side view.
PDB entry 6exn coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Postcatalytic spliceosome structure reveals mechanism of 3'-splice site selection.
Wilkinson ME, Fica SM, Galej WP, Norman CM, Newman AJ, Nagai K
Science 358 1283-1288 (2017)
PMID: 29146871
Related structures: EMD-3979

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
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
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 46-mer (preferred)
PDBe Complex ID:
PDB-CPX-294149 (preferred)
Entry contents:
31 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (36 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:
Splicing factor YJU2 Chain: D
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 ATP-dependent RNA helicase PRP22 Chain: V
U2 small nuclear ribonucleoprotein A' Chain: W
Unassigned structure Chain: X
U2 small nuclear ribonucleoprotein B'' Chain: Y
Pre-mRNA-splicing factor 18 Chain: a
Small nuclear ribonucleoprotein-associated protein B Chains: b, k
Pre-mRNA-splicing factor SLU7 Chain: c
Small nuclear ribonucleoprotein Sm D3 Chains: d, n
Small nuclear ribonucleoprotein E Chains: e, p
Small nuclear ribonucleoprotein F Chains: f, q
Small nuclear ribonucleoprotein G Chains: g, r
Small nuclear ribonucleoprotein Sm D1 Chains: h, l
Small nuclear ribonucleoprotein Sm D2 Chains: j, m
Pre-mRNA-processing factor 17 Chain: o
Pre-mRNA-splicing factor SNT309 Chain: s
Pre-mRNA-processing factor 19 Chains: t, u, v, w
Pre-mRNA-splicing factor SYF2 Chain: y
U2 snRNA Chain: 2
U5 snRNA Chain: 5
U6 snRNA Chain: 6
Ligated exons: UBC4 mRNA Chain: E
Intron lariat: UBC4 RNA Chain: I

Ligands and Environments

4 bound ligands:
Ligand MG 1 x MG
Ligand IHP 1 x IHP
Ligand GTP 1 x GTP
Ligand ZN 7 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.7Å
Relevant EMDB volumes: EMD-3979

Quick links

Citations

13 review citations

Structural Insights into Nuclear pre-mRNA Splicing in Higher Eukaryotes.
Kastner et al. (2019)
12 more

13 mentions without citation

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