› 5gmk

Electron Microscopy
3.4Å resolution

Cryo-EM structure of the Catalytic Step I spliceosome (C complex) at 3.4 angstrom resolution

Released:
DOI: 10.2210/pdb5gmk/pdb
PDB entry 5gmk coloured by chain, front view.
PDB entry 5gmk coloured by chain, side view.
PDB entry 5gmk coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structure of a yeast catalytic step I spliceosome at 3.4 Å resolution.
Wan R, Yan C, Bai R, Huang G, Shi Y
Science 353 895-904 (2016)
PMID: 27445308
Related structures: EMD-9525

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 45-mer (preferred)
PDBe Complex ID:
PDB-CPX-149219 (preferred)
Entry contents:
29 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (35 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
Molecule details ›
Chain: J
Length: 135 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q03375 (Residues: 1-135; Coverage: 100%)
Gene names: CWC21, YDR482C
Sequence domains: cwf21 domain
Pre-mRNA-splicing factor PRP46 Chain: O
Molecule details ›
Chain: O
Length: 451 amino acids
Theoretical weight: 50.77 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12417 (Residues: 1-451; Coverage: 100%)
Gene names: CWC1, NTC50, P2594, PRP46, YPL151C
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Pre-mRNA-processing protein 45 Chain: P
Molecule details ›
Chain: P
Length: 379 amino acids
Theoretical weight: 42.55 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P28004 (Residues: 1-379; Coverage: 100%)
Gene names: FUN20, PRP45, YAL032C
Sequence domains: SKIP/SNW domain
Pre-mRNA-splicing factor SLT11 Chain: Q
Molecule details ›
Chain: Q
Length: 364 amino acids
Theoretical weight: 40.99 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P38241 (Residues: 1-364; Coverage: 100%)
Gene names: ECM2, SLT11, YBR0614, YBR065C
Sequence domains: STL11, N-terminal
Pre-mRNA-splicing factor CWC2 Chain: R
Molecule details ›
Chain: R
Length: 339 amino acids
Theoretical weight: 38.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12046 (Residues: 1-339; Coverage: 100%)
Gene names: CWC2, D1041, NTC40, SLC3, YDL209C
Sequence domains:
Pre-mRNA-splicing factor CWC15 Chain: S
Molecule details ›
Chain: S
Length: 175 amino acids
Theoretical weight: 19.98 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q03772 (Residues: 1-175; Coverage: 100%)
Gene names: CWC15, YD8358.17, YDR163W
Sequence domains: Cwf15/Cwc15 cell cycle control protein
Pre-mRNA-splicing factor BUD31 Chain: T
Molecule details ›
Chain: T
Length: 157 amino acids
Theoretical weight: 18.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25337 (Residues: 1-157; Coverage: 100%)
Gene names: BUD31, CWC14, YCR063W, YCR63W, YCR903
Sequence domains: Pre-mRNA-splicing factor BUD31
Pre-mRNA-splicing factor CWC22 Chain: Z
Molecule details ›
Chain: Z
Length: 577 amino acids
Theoretical weight: 67.39 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53333 (Residues: 1-577; Coverage: 100%)
Gene names: CWC22, YGR278W
Sequence domains: MA3 domain
Pre-mRNA-splicing factor CEF1 Chain: c
Molecule details ›
Chain: c
Length: 587 amino acids
Theoretical weight: 61.06 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q03654 (Residues: 1-587; Coverage: 100%)
Gene names: CEF1, NTC85, YM8261.07, YMR213W
Sequence domains:
Pre-mRNA-splicing factor CLF1 Chain: d
Molecule details ›
Chain: d
Length: 687 amino acids
Theoretical weight: 68.04 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12309 (Residues: 1-275; Coverage: 40%)
Gene names: CLF1, L2952, NTC77, SYF3, YLR117C
Sequence domains: HAT (Half-A-TPR) repeat
Splicing factor YJU2 Chain: F
Molecule details ›
Chain: F
Length: 278 amino acids
Theoretical weight: 32.37 KDa
Source organism: Saccharomyces cerevisiae S288C
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: G
Molecule details ›
Chain: G
Length: 179 amino acids
Theoretical weight: 20.41 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53854 (Residues: 1-179; Coverage: 100%)
Gene names: CWC25, N0901, YNL245C
Sequence domains:
Pre-mRNA-splicing factor ISY1 Chain: H
Molecule details ›
Chain: H
Length: 235 amino acids
Theoretical weight: 28.07 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P21374 (Residues: 1-235; Coverage: 100%)
Gene names: ISY1, J1657, NTC30, UTR3, YJR050W
Sequence domains: Isy1-like splicing family
Pre-mRNA-splicing factor SYF2 Chain: I
Molecule details ›
Chain: I
Length: 215 amino acids
Theoretical weight: 24.85 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53277 (Residues: 1-215; Coverage: 100%)
Gene names: NTC31, SYF2, YGR129W
Sequence domains: SYF2 splicing factor
Pre-mRNA-splicing factor SYF1 Chain: v
Molecule details ›
Chain: v
Length: 859 amino acids
Theoretical weight: 78.13 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q04048 (Residues: 569-734; Coverage: 19%)
Gene names: NTC90, SYF1, YDR416W
Pre-mRNA-processing factor 17 Chain: n
Molecule details ›
Chain: n
Length: 455 amino acids
Theoretical weight: 52.13 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40968 (Residues: 1-455; Coverage: 100%)
Gene names: CDC40, D9481.11, PRP17, SLU4, XRS2, YDR364C
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Pre-mRNA-processing factor 19 Chains: o, p, q, r
Molecule details ›
Chains: o, p, q, r
Length: 503 amino acids
Theoretical weight: 56.63 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32523 (Residues: 1-503; Coverage: 100%)
Gene names: PRP19, PSO4, YLL036C
Sequence domains: Prp19/Pso4-like
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
Pre-mRNA-splicing factor SNT309 Chain: t
Molecule details ›
Chain: t
Length: 175 amino acids
Theoretical weight: 20.74 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06091 (Residues: 1-175; Coverage: 100%)
Gene names: NTC25, SNT309, YPR101W
Small nuclear ribonucleoprotein-associated protein B Chains: k, s
Molecule details ›
Chains: k, s
Length: 196 amino acids
Theoretical weight: 22.43 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40018 (Residues: 1-196; Coverage: 100%)
Gene names: SMB1, YER029C
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chains: i, u
Molecule details ›
Chains: i, u
Length: 94 amino acids
Theoretical weight: 10.39 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q12330 (Residues: 1-94; Coverage: 100%)
Gene names: SME1, YOR159C
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein F Chains: h, w
Molecule details ›
Chains: h, w
Length: 86 amino acids
Theoretical weight: 9.67 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P54999 (Residues: 1-86; Coverage: 100%)
Gene names: P9705.4, SMX3, YPR182W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein G Chains: j, x
Molecule details ›
Chains: j, x
Length: 77 amino acids
Theoretical weight: 8.49 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40204 (Residues: 1-77; Coverage: 100%)
Gene names: SMX2, SNP2, YFL017Bw, YFL017W-A
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D3 Chains: l, y
Molecule details ›
Chains: l, y
Length: 101 amino acids
Theoretical weight: 11.24 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P43321 (Residues: 1-101; Coverage: 100%)
Gene names: L9634.6, SMD3, YLR147C
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D1 Chains: m, z
Molecule details ›
Chains: m, z
Length: 146 amino acids
Theoretical weight: 16.3 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02260 (Residues: 1-146; Coverage: 100%)
Gene names: SMD1, YGR074W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D2 Chains: e, g
Molecule details ›
Chains: e, g
Length: 110 amino acids
Theoretical weight: 12.88 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06217 (Residues: 1-110; Coverage: 100%)
Gene names: L9328.5, SMD2, YLR275W
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U2 small nuclear ribonucleoprotein B'' Chain: a
Molecule details ›
Chain: a
Length: 111 amino acids
Theoretical weight: 12.85 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40567 (Residues: 1-111; Coverage: 100%)
Gene names: MSL1, YIB9W, YIR009W
Sequence domains: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
Structure domains: Alpha-Beta Plaits
U2 small nuclear ribonucleoprotein A' Chain: b
Molecule details ›
Chain: b
Length: 238 amino acids
Theoretical weight: 27.23 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q08963 (Residues: 1-238; Coverage: 100%)
Gene names: LEA1, YPL213W
Sequence domains: Leucine-rich repeat
U5 snRNA Chain: D
Molecule details ›
Chain: D
Length: 214 nucleotides
Theoretical weight: 68.64 KDa
Sequence domains: U5 spliceosomal RNA
U6 snRNA Chain: E
Molecule details ›
Chain: E
Length: 112 nucleotides
Theoretical weight: 35.88 KDa
Sequence domains: U6 spliceosomal RNA
U2 snRNA Chain: L
Molecule details ›
Chain: L
Length: 1175 nucleotides
Theoretical weight: 376.27 KDa
Sequence domains: U2 spliceosomal RNA
Intron_BPS Chain: M
Molecule details ›
Chain: M
Length: 29 nucleotides
Theoretical weight: 9.16 KDa
5'-Exon Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 4.11 KDa
5'-Splicing Site Chain: N
Molecule details ›
Chain: N
Length: 15 nucleotides
Theoretical weight: 4.69 KDa

Ligands and Environments

3 bound ligands:
Ligand GTP 1 x GTP
Ligand MG 6 x MG
Ligand ZN 7 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-9525

Quick links

Citations

30 review citations

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

20 mentions without citation

Molecular Mechanisms of pre-mRNA Splicing through Structural Biology of the Spliceosome.
Yan et al. (2019)
19 more