› 5lj3

Electron Microscopy
3.8Å resolution

Structure of the core of the yeast spliceosome immediately after branching

Released:
DOI: 10.2210/pdb5lj3/pdb
PDB entry 5lj3 coloured by chain, front view.
PDB entry 5lj3 coloured by chain, side view.
PDB entry 5lj3 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Cryo-EM structure of the spliceosome immediately after branching.
Galej WP, Wilkinson ME, Fica SM, Oubridge C, Newman AJ, Nagai K
OpenAccess logo Nature 537 197-201 (2016)
PMID: 27459055
Related structures: EMD-4055

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 38-mer (preferred)
PDBe Complex ID:
PDB-CPX-149221 (preferred)
Entry contents:
26 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (31 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:
Splicing factor YJU2 Chain: D
Molecule details ›
Chain: D
Length: 278 amino acids
Theoretical weight: 32.37 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P28320 (Residues: 1-278; Coverage: 100%)
Gene names: CWC16, YJU2, YKL095W, YKL442
Sequence domains: Saf4/Yju2 protein
Pre-mRNA-splicing factor CWC25 Chain: F
Pre-mRNA-splicing factor SNU114 Chain: C
Pre-mRNA-splicing factor ISY1 Chain: G
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
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
U2 small nuclear ribonucleoprotein A' Chain: W
U2 small nuclear ribonucleoprotein B'' Chain: Y
unknown Chain: x
U5 snRNA (small nuclear RNA) Chain: U
Exon 1 (5' exon) of UBC4 pre-mRNA Chain: E
Intron of UBC4 pre-mRNA Chain: I
U2 snRNA (small nuclear RNA) Chain: Z
U6 snRNA (small nuclear RNA) Chain: V

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand ZN 7 x ZN
Ligand GTP 1 x GTP
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.8Å
Relevant EMDB volumes: EMD-4055

Quick links

Citations

37 review citations

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

21 mentions without citation

Structural and functional modularity of the U2 snRNP in pre-mRNA splicing.
van der Feltz et al. (2019)
20 more