› 5mq0

Electron Microscopy
4.17Å resolution

Structure of a spliceosome remodeled for exon ligation

Released:
DOI: 10.2210/pdb5mq0/pdb
PDB entry 5mq0 coloured by chain, front view.
PDB entry 5mq0 coloured by chain, side view.
PDB entry 5mq0 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure of a spliceosome remodelled for exon ligation.
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K
OpenAccess logo Nature 542 377-380 (2017)
PMID: 28076345
Related structures: EMD-3541

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
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 46-mer (preferred)
PDBe Complex ID:
PDB-CPX-150217 (preferred)
Entry contents:
30 distinct polypeptide molecules
6 distinct RNA molecules
Macromolecules (36 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 factor SNU114 Chain: C
Molecule details ›
Chain: C
Length: 1008 amino acids
Theoretical weight: 114.17 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36048 (Residues: 1-1008; Coverage: 100%)
Gene names: GIN10, SNU114, YKL173W, YKL637
Sequence domains:
Pre-mRNA-splicing factor CWC22 Chain: H
Molecule details ›
Chain: H
Length: 577 amino acids
Theoretical weight: 67.39 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P53333 (Residues: 1-577; Coverage: 100%)
Gene names: CWC22, YGR278W
Sequence domains: MA3 domain
Pre-mRNA-splicing factor PRP46 Chain: J
Molecule details ›
Chain: J
Length: 451 amino acids
Theoretical weight: 50.77 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12417 (Residues: 1-451; Coverage: 100%)
Gene names: CWC1, NTC50, P2594, PRP46, YPL151C
Sequence domains: WD domain, G-beta repeat
Pre-mRNA-processing protein 45 Chain: K
Molecule details ›
Chain: K
Length: 379 amino acids
Theoretical weight: 42.55 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P28004 (Residues: 1-379; Coverage: 100%)
Gene names: FUN20, PRP45, YAL032C
Sequence domains: SKIP/SNW domain
Pre-mRNA-splicing factor BUD31 Chain: L
Molecule details ›
Chain: L
Length: 157 amino acids
Theoretical weight: 18.48 KDa
Source organism: Saccharomyces cerevisiae
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 CWC2 Chain: M
Molecule details ›
Chain: M
Length: 339 amino acids
Theoretical weight: 38.49 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12046 (Residues: 1-339; Coverage: 100%)
Gene names: CWC2, D1041, NTC40, SLC3, YDL209C
Sequence domains:
Pre-mRNA-splicing factor SLT11 Chain: N
Molecule details ›
Chain: N
Length: 364 amino acids
Theoretical weight: 40.99 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38241 (Residues: 1-364; Coverage: 100%)
Gene names: ECM2, SLT11, YBR0614, YBR065C
Sequence domains: STL11, N-terminal
Pre-mRNA-splicing factor CEF1 Chain: O
Molecule details ›
Chain: O
Length: 590 amino acids
Theoretical weight: 67.84 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03654 (Residues: 1-590; Coverage: 100%)
Gene names: CEF1, NTC85, YM8261.07, YMR213W
Sequence domains:
Pre-mRNA-splicing factor CWC15 Chain: P
Molecule details ›
Chain: P
Length: 175 amino acids
Theoretical weight: 19.98 KDa
Source organism: Saccharomyces cerevisiae
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 CWC21 Chain: R
Molecule details ›
Chain: R
Length: 135 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q03375 (Residues: 1-135; Coverage: 100%)
Gene names: CWC21, YDR482C
Sequence domains: cwf21 domain
Pre-mRNA-splicing factor CLF1 Chain: S
Molecule details ›
Chain: S
Length: 687 amino acids
Theoretical weight: 82.56 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12309 (Residues: 1-687; Coverage: 100%)
Gene names: CLF1, L2952, NTC77, SYF3, YLR117C
Sequence domains: Suppressor of forked protein (Suf)
Pre-mRNA-splicing factor SYF1 Chain: T
Molecule details ›
Chain: T
Length: 877 amino acids
Theoretical weight: 101.88 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04048 (Residues: 1-859; Coverage: 100%)
Gene names: NTC90, SYF1, YDR416W
Sequence domains: Suppressor of forked protein (Suf)
Pre-mRNA-splicing factor 18 Chain: a
Molecule details ›
Chain: a
Length: 251 amino acids
Theoretical weight: 28.41 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P33411 (Residues: 1-251; Coverage: 100%)
Gene names: PRP18, YGR006W
Sequence domains: Prp18 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
UniProt:
  • Canonical: Q02775 (Residues: 1-382; Coverage: 100%)
Gene names: D4483, SLT17, SLU7, YDR088C
Sequence domains: Pre-mRNA splicing Prp18-interacting factor
Pre-mRNA-processing factor 17 Chain: o
Molecule details ›
Chain: o
Length: 455 amino acids
Theoretical weight: 52.13 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40968 (Residues: 1-455; Coverage: 100%)
Gene names: CDC40, D9481.11, PRP17, SLU4, XRS2, YDR364C
Sequence domains: WD domain, G-beta repeat
UNKNOWN PROTEIN Chain: X
Molecule details ›
Chain: X
Length: 68 amino acids
Theoretical weight: 5.81 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
UniProt:
  • Canonical: P53277 (Residues: 1-215; Coverage: 100%)
Gene names: NTC31, SYF2, YGR129W
Sequence domains: SYF2 splicing factor
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
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
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22 Chain: V
Molecule details ›
Chain: V
Length: 1145 amino acids
Theoretical weight: 130.19 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P24384 (Residues: 1-1145; Coverage: 100%)
Gene names: PRP22, YER013W
Sequence domains:
U2 small nuclear ribonucleoprotein A' Chain: W
Molecule details ›
Chain: W
Length: 238 amino acids
Theoretical weight: 27.23 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q08963 (Residues: 1-238; Coverage: 100%)
Gene names: LEA1, YPL213W
Sequence domains: Leucine-rich repeat
U2 small nuclear ribonucleoprotein B'' Chain: Y
Molecule details ›
Chain: Y
Length: 111 amino acids
Theoretical weight: 12.85 KDa
Source organism: Saccharomyces cerevisiae
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)
Pre-mRNA-splicing factor SNT309 Chain: s
Molecule details ›
Chain: s
Length: 175 amino acids
Theoretical weight: 20.74 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06091 (Residues: 1-175; Coverage: 100%)
Gene names: NTC25, SNT309, YPR101W
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
UniProt:
  • Canonical: P32523 (Residues: 1-503; Coverage: 100%)
Gene names: PRP19, PSO4, YLL036C
Sequence domains: Prp19/Pso4-like
Yeast UBC4 gene for ubiquitin-conjugating enzyme Chain: I
Molecule details ›
Chain: I
Length: 95 nucleotides
Theoretical weight: 30.2 KDa
5'-EXON OF UBC4 PRE-MRNA Chain: E
Molecule details ›
Chain: E
Length: 20 nucleotides
Theoretical weight: 6.52 KDa
S.cerevisiae chromosome II reading frame ORF YBR230c Chain: 2
Molecule details ›
Chain: 2
Length: 1175 nucleotides
Theoretical weight: 376.27 KDa
Sequence domains: U2 spliceosomal RNA
Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence Chain: 6
Molecule details ›
Chain: 6
Length: 112 nucleotides
Theoretical weight: 35.88 KDa
Sequence domains: U6 spliceosomal RNA
Saccharomyces cerevisiae strain WI_C_MBSP_4 chromosome VII sequence Chain: 5
Molecule details ›
Chain: 5
Length: 179 nucleotides
Theoretical weight: 57.44 KDa
Sequence domains: U5 spliceosomal RNA
3'-EXON OF UBC4 PRE-MRNA, BOUND BY PRP22 HELICASE Chain: 3
Molecule details ›
Chain: 3
Length: 3 nucleotides
Theoretical weight: 874 Da

Ligands and Environments

5 bound ligands:
Ligand MG 3 x MG
Ligand K 2 x K
Ligand IHP 1 x IHP
Ligand GTP 1 x GTP
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.17Å
Relevant EMDB volumes: EMD-3541

Quick links

Citations

27 review citations

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

11 mentions without citation

Cryo-electron microscopy snapshots of the spliceosome: structural insights into a dynamic ribonucleoprotein machine.
Fica et al. (2017)
10 more