› 5gm6

Electron Microscopy
3.5Å resolution

Cryo-EM structure of the activated spliceosome (Bact complex) at 3.5 angstrom resolution

Released:
DOI: 10.2210/pdb5gm6/pdb
PDB entry 5gm6 coloured by chain, front view.
PDB entry 5gm6 coloured by chain, side view.
PDB entry 5gm6 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structure of a yeast activated spliceosome at 3.5 Å resolution.
Yan C, Wan R, Bai R, Huang G, Shi Y
Science 353 904-11 (2016)
PMID: 27445306
Related structures: EMD-9524

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
Peptidylproline (omega=180) = peptidylproline (omega=0)
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)
Assembly name:
PDBe Complex ID:
PDB-CPX-142864 (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: 2287 amino acids
Theoretical weight: 265.95 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P33334 (Residues: 128-2413; Coverage: 95%)
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 S288C
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 S288C
UniProt:
  • Canonical: P36048 (Residues: 1-1008; Coverage: 100%)
Gene names: GIN10, SNU114, YKL173W, YKL637
Sequence domains:
Pre-mRNA-splicing factor RSE1 Chain: F
Molecule details ›
Chain: F
Length: 1361 amino acids
Theoretical weight: 153.96 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q04693 (Residues: 1-1361; Coverage: 100%)
Gene names: RSE1, SAP130, YM9827.03C, YML049C
Sequence domains:
Cold sensitive U2 snRNA suppressor 1 Chain: H
Molecule details ›
Chain: H
Length: 436 amino acids
Theoretical weight: 50.34 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02554 (Residues: 1-436; Coverage: 100%)
Gene names: CUS1, YM9408.02C, YMR240C
Sequence domains:
Pre-mRNA-splicing factor PRP11 Chain: I
Molecule details ›
Chain: I
Length: 266 amino acids
Theoretical weight: 29.96 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q07350 (Residues: 1-266; Coverage: 100%)
Gene names: D2711, PRP10, PRP11, RNA11, YDL043C
Sequence domains:
Pre-mRNA-splicing factor RDS3 Chain: J
Molecule details ›
Chain: J
Length: 107 amino acids
Theoretical weight: 12.28 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06835 (Residues: 1-107; Coverage: 100%)
Gene names: P9513.2, RDS3, YPR094W
Sequence domains: PHF5-like protein
RDS3 complex subunit 10 Chain: K
Molecule details ›
Chain: K
Length: 85 amino acids
Theoretical weight: 10.05 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P0C074 (Residues: 1-85; Coverage: 100%)
Gene names: RCP10, YNL138W-A, YSF3
Sequence domains: Splicing factor 3B subunit 10 (SF3b10)
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
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 leakage protein 1 Chain: U
Molecule details ›
Chain: U
Length: 207 amino acids
Theoretical weight: 24.1 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q07930 (Residues: 1-204; Coverage: 100%)
Gene names: L1591, PML1, YLR016C
Sequence domains: FHA domain
U2 snRNP component IST3 Chain: V
Molecule details ›
Chain: V
Length: 148 amino acids
Theoretical weight: 17.12 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P40565 (Residues: 1-148; Coverage: 100%)
Gene names: IST3, SNU17, YIB5W, YIR005W
Sequence domains: RNA recognition motif
Pre-mRNA-splicing factor CWC26 Chain: W
Molecule details ›
Chain: W
Length: 266 amino acids
Theoretical weight: 30.53 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P46947 (Residues: 1-266; Coverage: 100%)
Gene names: BUD13, CWC26, G1642, SLC7, YGL174W
Sequence domains: Pre-mRNA-splicing factor of RES complex
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 Chain: Y
Molecule details ›
Chain: Y
Length: 876 amino acids
Theoretical weight: 99.95 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P20095 (Residues: 1-876; Coverage: 100%)
Gene names: N2048, PRP2, RNA2, YNR011C
Sequence domains:
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 CWC24 Chain: a
Molecule details ›
Chain: a
Length: 259 amino acids
Theoretical weight: 29.8 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P53769 (Residues: 1-259; Coverage: 100%)
Gene names: CWC24, L8543.3, YLR323C
Sequence domains:
Peptidyl-prolyl isomerase CWC27 Chain: b
Molecule details ›
Chain: b
Length: 301 amino acids
Theoretical weight: 35.08 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q02770 (Residues: 1-301; Coverage: 100%)
Gene names: CWC27, CYP7, YPL064C
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
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:
U2 snRNP component HSH155 Chain: G
Molecule details ›
Chain: G
Length: 971 amino acids
Theoretical weight: 110.17 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P49955 (Residues: 1-971; Coverage: 100%)
Gene names: HSH155, YM8021.14, YMR288W
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
Pre-mRNA-splicing factor CWC21 Chain: X
Molecule details ›
Chain: X
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 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
Protein HSH49 Chain: e
Molecule details ›
Chain: e
Length: 213 amino acids
Theoretical weight: 24.53 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q99181 (Residues: 1-213; Coverage: 100%)
Gene names: HSH49, O6142, YOR319W
Sequence domains: RNA recognition motif
Pre-mRNA-splicing factor SYF2 Chain: f
Molecule details ›
Chain: f
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-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
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
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
Small nuclear ribonucleoprotein-associated protein B Chain: k
Molecule details ›
Chain: k
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 Chain: i
Molecule details ›
Chain: i
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
Small nuclear ribonucleoprotein F Chain: h
Molecule details ›
Chain: h
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
Small nuclear ribonucleoprotein G Chain: j
Molecule details ›
Chain: j
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
Small nuclear ribonucleoprotein Sm D3 Chain: l
Molecule details ›
Chain: l
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
Small nuclear ribonucleoprotein Sm D1 Chain: m
Molecule details ›
Chain: m
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
Small nuclear ribonucleoprotein Sm D2 Chain: g
Molecule details ›
Chain: g
Length: 94 amino acids
Theoretical weight: 11.02 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q06217 (Residues: 15-108; Coverage: 86%)
Gene names: L9328.5, SMD2, YLR275W
Sequence domains: LSM domain
Saccharomyces cerevisiae strain CDRDR_sf_H chromosome VII sequence Chain: D
Molecule details ›
Chain: D
Length: 214 nucleotides
Theoretical weight: 68.64 KDa
Sequence domains: U5 spliceosomal RNA
Saccharomyces cerevisiae strain T.52_2H chromosome XII sequence 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
Pre-mRNA Chain: N
Molecule details ›
Chain: N
Length: 25 nucleotides
Theoretical weight: 7.86 KDa
Pre-mRNA Chain: M
Molecule details ›
Chain: M
Length: 61 nucleotides
Theoretical weight: 18.92 KDa

Ligands and Environments

4 bound ligands:
Ligand GTP 1 x GTP
Ligand MG 5 x MG
Ligand ZN 13 x ZN
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-9524

Quick links

Citations

29 review citations

Circular RNAs in human cancer.
Wang et al. (2017)
28 more

39 mentions without citation

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