› 5mq0

Electron Microscopy
4.17Å resolution

Structure of a spliceosome remodeled for exon ligation

Released:
DOI: 10.2210/pdb5mq0/pdb
PDB entry 5mq0 coloured by chain, front view.
PDB entry 5mq0 coloured by chain, side view.
PDB entry 5mq0 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-3541

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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 46-mer (preferred)
PDBe Complex ID:
PDB-CPX-150217 (preferred)
Entry contents:
30 distinct polypeptide molecules
6 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
Pre-mRNA-splicing factor SNU114 Chain: C
Molecule details ›
Chain: C
Length: 1008 amino acids
Theoretical weight: 114.17 KDa
Source organism: Saccharomyces cerevisiae
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 PROTEIN Chain: X
Pre-mRNA-splicing factor SYF2 Chain: y
Small nuclear ribonucleoprotein-associated protein B Chains: b, k
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-splicing factor ATP-dependent RNA helicase PRP22 Chain: V
U2 small nuclear ribonucleoprotein A' Chain: W
U2 small nuclear ribonucleoprotein B'' Chain: Y
Pre-mRNA-splicing factor SNT309 Chain: s
Pre-mRNA-processing factor 19 Chains: t, u, v, w
Yeast UBC4 gene for ubiquitin-conjugating enzyme Chain: I
5'-EXON OF UBC4 PRE-MRNA Chain: E
S.cerevisiae chromosome II reading frame ORF YBR230c Chain: 2
Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence Chain: 6
Saccharomyces cerevisiae strain WI_C_MBSP_4 chromosome VII sequence Chain: 5
3'-EXON OF UBC4 PRE-MRNA, BOUND BY PRP22 HELICASE Chain: 3

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

Entry percentile scores
Resolution: 4.17Å
Relevant EMDB volumes: EMD-3541
Expression system: in vitro transcription vector pT7-Fluc(deltai)

Quick links

Citations

27 review citations

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

11 mentions without citation

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine.
Fica et al. (2017)
10 more

Experimental raw data

Links to raw experimental data available for this entry are listed below

Electron microscopy data related to PDB entry 5mq0 found at the Electron Microscopy Public Image Archive (EMPIAR)

Data DOI: 10.6019/EMPIAR-10687
Datasets: 10
Total size: 8900Gb
EMPIAR thumbnail