› 6j6h

Electron Microscopy
3.6Å resolution

Cryo-EM structure of the yeast B*-a1 complex at an average resolution of 3.6 angstrom

Released:
DOI: 10.2210/pdb6j6h/pdb
PDB entry 6j6h coloured by chain, front view.
PDB entry 6j6h coloured by chain, side view.
PDB entry 6j6h coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structures of the Catalytically Activated Yeast Spliceosome Reveal the Mechanism of Branching.
Wan R, Bai R, Yan C, Lei J, Shi Y
Cell 177 339-351.e13 (2019)
PMID: 30879786
Related structures: EMD-0687

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 41-mer (preferred)
PDBe Complex ID:
PDB-CPX-149223 (preferred)
Entry contents:
27 distinct polypeptide molecules
4 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 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-processing factor 17 Chain: n
Pre-mRNA-splicing factor ISY1 Chain: H
Pre-mRNA-splicing factor SYF1 Chain: v
U2 small nuclear ribonucleoprotein B'' Chain: a
U2 small nuclear ribonucleoprotein A' Chain: b
Pre-mRNA-splicing factor SNT309 Chain: t
Small nuclear ribonucleoprotein E Chains: i, u
Small nuclear ribonucleoprotein Sm D1 Chains: m, z
Small nuclear ribonucleoprotein G Chains: j, x
Small nuclear ribonucleoprotein F Chains: h, w
Small nuclear ribonucleoprotein Sm D2 Chains: e, g
Small nuclear ribonucleoprotein-associated protein B Chains: k, s
Small nuclear ribonucleoprotein Sm D3 Chains: l, y
Pre-mRNA-processing factor 19 Chains: o, p, q, r
ACT1 pre-mRNA Chain: B
U5 snRNA Chain: D
U6 snRNA Chain: E
U2 snRNA Chain: L

Ligands and Environments

4 bound ligands:
Ligand IHP 1 x IHP
Ligand GTP 1 x GTP
Ligand MG 6 x MG
Ligand ZN 6 x ZN
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-0687

Quick links

Citations

7 review citations

Regulation of pre-mRNA splicing: roles in physiology and disease, and therapeutic prospects.
Rogalska et al. (2023)
6 more

3 mentions without citation

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