› 7b9v

Electron Microscopy
2.8Å resolution

Yeast C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound

Released:
DOI: 10.2210/pdb7b9v/pdb
PDB entry 7b9v coloured by chain, front view.
PDB entry 7b9v coloured by chain, side view.
PDB entry 7b9v coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis for conformational equilibrium of the catalytic spliceosome.
Wilkinson ME, Fica SM, Galej WP, Nagai K
OpenAccess logo Mol Cell 81 1439-1452.e9 (2021)
PMID: 33705709
Related structures: EMD-12106

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 50-mer (preferred)
PDBe Complex ID:
PDB-CPX-247686 (preferred)
Entry contents:
35 distinct polypeptide molecules
5 distinct RNA molecules
Macromolecules (40 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:
Pre-mRNA-splicing helicase BRR2 Chain: B
Molecule details ›
Chain: B
Length: 2163 amino acids
Theoretical weight: 246.47 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P32639 (Residues: 1-2163; Coverage: 100%)
Gene names: BRR2, RSS1, SNU246, SYGP-ORF66, YER172C
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
Splicing factor YJU2 Chain: D
Molecule details ›
Chain: D
Length: 291 amino acids
Theoretical weight: 33.36 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-splicing factor CWC25 Chain: F
Molecule details ›
Chain: F
Length: 179 amino acids
Theoretical weight: 20.01 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-splicing factor ISY1 Chain: G
Molecule details ›
Chain: G
Length: 235 amino acids
Theoretical weight: 27.63 KDa
Source organism: Saccharomyces cerevisiae
CWC22 isoform 1 Chain: H
Molecule details ›
Chain: H
Length: 577 amino acids
Theoretical weight: 67.39 KDa
Source organism: Saccharomyces cerevisiae
BJ4_G0054360.mRNA.1.CDS.1 Chain: J
Molecule details ›
Chain: J
Length: 451 amino acids
Theoretical weight: 50.77 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-processing protein 45 Chain: K
Molecule details ›
Chain: K
Length: 379 amino acids
Theoretical weight: 42.55 KDa
Source organism: Saccharomyces cerevisiae
BUD31 isoform 1 Chain: L
Molecule details ›
Chain: L
Length: 157 amino acids
Theoretical weight: 18.48 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-splicing factor CWC2 Chain: M
Molecule details ›
Chain: M
Length: 339 amino acids
Theoretical weight: 38.49 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-splicing factor SLT11 Chain: N
Molecule details ›
Chain: N
Length: 364 amino acids
Theoretical weight: 40.99 KDa
Source organism: Saccharomyces cerevisiae
Y55_G0042700.mRNA.1.CDS.1 Chain: O
Molecule details ›
Chain: O
Length: 590 amino acids
Theoretical weight: 67.09 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-splicing factor CWC15 Chain: P
Molecule details ›
Chain: P
Length: 175 amino acids
Theoretical weight: 19.98 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16 Chain: Q
Molecule details ›
Chain: Q
Length: 1071 amino acids
Theoretical weight: 121.82 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-splicing factor CWC21 Chain: R
Molecule details ›
Chain: R
Length: 135 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae
CLF1 isoform 1 Chain: S
Molecule details ›
Chain: S
Length: 687 amino acids
Theoretical weight: 82.56 KDa
Source organism: Saccharomyces cerevisiae
SYF1 isoform 1 Chain: T
Molecule details ›
Chain: T
Length: 859 amino acids
Theoretical weight: 100.34 KDa
Source organism: Saccharomyces cerevisiae
HLJ1_G0053790.mRNA.1.CDS.1 Chain: W
Molecule details ›
Chain: W
Length: 238 amino acids
Theoretical weight: 27.23 KDa
Source organism: Saccharomyces cerevisiae
Unassigned structure Chain: X
Molecule details ›
Chain: X
Length: 240 amino acids
Theoretical weight: 20.44 KDa
Source organism: Saccharomyces cerevisiae
BJ4_G0027490.mRNA.1.CDS.1 Chain: Y
Molecule details ›
Chain: Y
Length: 111 amino acids
Theoretical weight: 12.85 KDa
Source organism: Saccharomyces cerevisiae
NTC20 isoform 1 Chain: Z
Molecule details ›
Chain: Z
Length: 140 amino acids
Theoretical weight: 15.99 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-splicing factor 18 Chain: a
Molecule details ›
Chain: a
Length: 251 amino acids
Theoretical weight: 28.41 KDa
Source organism: Saccharomyces cerevisiae
Small nuclear ribonucleoprotein-associated protein B Chains: b, k
Molecule details ›
Chains: b, k
Length: 196 amino acids
Theoretical weight: 22.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40018 (Residues: 1-196; Coverage: 100%)
Gene names: SMB1, YER029C
Sequence domains: LSM domain
Pre-mRNA-splicing factor SLU7 Chain: c
Molecule details ›
Chain: c
Length: 382 amino acids
Theoretical weight: 44.72 KDa
Source organism: Saccharomyces cerevisiae
Small nuclear ribonucleoprotein Sm D3 Chains: d, n
Molecule details ›
Chains: d, n
Length: 101 amino acids
Theoretical weight: 11.24 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P43321 (Residues: 1-101; Coverage: 100%)
Gene names: L9634.6, SMD3, YLR147C
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chains: e, p
Molecule details ›
Chains: e, p
Length: 94 amino acids
Theoretical weight: 10.39 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12330 (Residues: 1-94; Coverage: 100%)
Gene names: SME1, YOR159C
Sequence domains: LSM domain
Small nuclear ribonucleoprotein F Chains: f, q
Molecule details ›
Chains: f, q
Length: 86 amino acids
Theoretical weight: 9.67 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P54999 (Residues: 1-86; Coverage: 100%)
Gene names: P9705.4, SMX3, YPR182W
Sequence domains: LSM domain
Small nuclear ribonucleoprotein G Chains: g, r
Molecule details ›
Chains: g, r
Length: 77 amino acids
Theoretical weight: 8.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40204 (Residues: 1-77; Coverage: 100%)
Gene names: SMX2, SNP2, YFL017Bw, YFL017W-A
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chains: h, l
Molecule details ›
Chains: h, l
Length: 146 amino acids
Theoretical weight: 16.3 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02260 (Residues: 1-146; Coverage: 100%)
Gene names: SMD1, YGR074W
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D2 Chains: j, m
Molecule details ›
Chains: j, m
Length: 110 amino acids
Theoretical weight: 12.88 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06217 (Residues: 1-110; Coverage: 100%)
Gene names: L9328.5, SMD2, YLR275W
Sequence domains: LSM domain
CDC40 isoform 1 Chain: o
Molecule details ›
Chain: o
Length: 455 amino acids
Theoretical weight: 52.21 KDa
Source organism: Saccharomyces cerevisiae
SNT309 isoform 1 Chain: s
Molecule details ›
Chain: s
Length: 175 amino acids
Theoretical weight: 20.74 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-processing factor 19 Chains: t, u, v, w
Molecule details ›
Chains: t, u, v, w
Length: 503 amino acids
Theoretical weight: 56.63 KDa
Source organism: Saccharomyces cerevisiae
Pre-mRNA-splicing factor SYF2 Chain: y
Molecule details ›
Chain: y
Length: 215 amino acids
Theoretical weight: 24.85 KDa
Source organism: Saccharomyces cerevisiae
U2 snRNA Chain: 2
Molecule details ›
Chain: 2
Length: 1175 nucleotides
Theoretical weight: 376.27 KDa
Sequence domains: U2 spliceosomal RNA
U5 snRNA Chain: 5
Molecule details ›
Chain: 5
Length: 214 nucleotides
Theoretical weight: 68.64 KDa
Sequence domains: U5 spliceosomal RNA
U6 snRNA Chain: 6
Molecule details ›
Chain: 6
Length: 112 nucleotides
Theoretical weight: 35.88 KDa
Sequence domains: U6 spliceosomal RNA
5' exon of UBC4 mRNA Chain: E
Molecule details ›
Chain: E
Length: 47 nucleotides
Theoretical weight: 15.04 KDa
Branched intron and 3' exon of UBC4 pre-mRNA Chain: I
Molecule details ›
Chain: I
Length: 95 nucleotides
Theoretical weight: 30.2 KDa

Ligands and Environments

5 bound ligands:
Ligand MG 6 x MG
Ligand K 1 x K
Ligand KGN 1 x KGN
Ligand GTP 1 x GTP
Ligand ZN 8 x ZN
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
Resolution: 2.8Å
Relevant EMDB volumes: EMD-12106

Quick links

Citations

3 review citations

Structural studies of the spliceosome: Bridging the gaps.
Tholen et al. (2022)
2 more

6 mentions without citation

Structural basis for conformational equilibrium of the catalytic spliceosome.
Wilkinson et al. (2021)
5 more