› 5zwm

Electron Microscopy
3.4Å resolution

Cryo-EM structure of the yeast pre-B complex at an average resolution of 3.4~4.6 angstrom (tri-snRNP and U2 snRNP Part)

Released:
DOI: 10.2210/pdb5zwm/pdb
PDB entry 5zwm coloured by chain, front view.
PDB entry 5zwm coloured by chain, side view.
PDB entry 5zwm coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structures of the fully assembled Saccharomyces cerevisiae spliceosome before activation.
Bai R, Wan R, Yan C, Lei J, Shi Y
Science 360 1423-1429 (2018)
PMID: 29794219
Related structures: EMD-6972

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142860 (preferred)
Entry contents:
38 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (43 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:
U4/U6 small nuclear ribonucleoprotein PRP4 Chain: K
Molecule details ›
Chain: K
Length: 465 amino acids
Theoretical weight: 52.51 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P20053 (Residues: 1-465; Coverage: 100%)
Gene names: P9705.6, PRP4, RNA4, YPR178W
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-processing factor 31 Chain: L
Pre-mRNA-splicing factor 6 Chain: N
U4/U6 small nuclear ribonucleoprotein PRP3 Chain: J
Spliceosomal protein DIB1 Chain: E
13 kDa ribonucleoprotein-associated protein Chain: M
Pre-mRNA-splicing factor SNU114 Chain: C
U6 snRNA-associated Sm-like protein LSm8 Chain: z
U6 snRNA-associated Sm-like protein LSm2 Chain: q
U6 snRNA-associated Sm-like protein LSm3 Chain: r
U6 snRNA-associated Sm-like protein LSm6 Chain: x
U6 snRNA-associated Sm-like protein LSm5 Chain: t
U6 snRNA-associated Sm-like protein LSm7 Chain: y
U6 snRNA-associated Sm-like protein LSm4 Chain: s
66 kDa U4/U6.U5 small nuclear ribonucleoprotein component Chain: O
Small nuclear ribonucleoprotein Sm D3 Chains: S, d, l
Small nuclear ribonucleoprotein-associated protein B Chains: P, a, h
Small nuclear ribonucleoprotein Sm D1 Chains: Q, b, m
Small nuclear ribonucleoprotein Sm D2 Chains: R, c, n
Small nuclear ribonucleoprotein E Chains: T, e, i
Small nuclear ribonucleoprotein F Chains: U, f, j
Small nuclear ribonucleoprotein G Chains: V, g, k
Pre-mRNA-splicing helicase BRR2 Chain: D
U2 small nuclear ribonucleoprotein A' Chain: o
U2 small nuclear ribonucleoprotein B'' Chain: p
U2 snRNP component HSH155 Chain: 1
Cold sensitive U2 snRNA suppressor 1 Chain: 2
Pre-mRNA-splicing factor RSE1 Chain: 3
Protein HSH49 Chain: 4
Pre-mRNA-splicing factor RDS3 Chain: 5
RDS3 complex subunit 10 Chain: 6
U2 snRNP component IST3 Chain: X
Pre-mRNA-splicing factor CWC26 Chain: Y
Pre-mRNA leakage protein 1 Chain: Z
Pre-mRNA-splicing factor PRP9 Chain: u
Pre-mRNA-splicing factor PRP21 Chain: w
Pre-mRNA-splicing factor PRP11 Chain: v
U6 snRNA Chain: F
U4 snRNA Chain: I
U5 snRNA Chain: B
Pre-mRNA-BPS Chain: G
U2 snRNA Chain: H

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-6972

Quick links

Citations

9 review citations

Roles and mechanisms of alternative splicing in cancer - implications for care.
Bonnal et al. (2020)
8 more

5 mentions without citation

Structures of SF3b1 reveal a dynamic Achilles heel of spliceosome assembly: Implications for cancer-associated abnormalities and drug discovery.
Maji et al. (2019)
4 more