› 5lqw

Electron Microscopy
5.8Å resolution

yeast activated spliceosome

Released:
DOI: 10.2210/pdb5lqw/pdb
PDB entry 5lqw coloured by chain, front view.
PDB entry 5lqw coloured by chain, side view.
PDB entry 5lqw coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Molecular architecture of the Saccharomyces cerevisiae activated spliceosome.
Rauhut R, Fabrizio P, Dybkov O, Hartmuth K, Pena V, Chari A, Kumar V, Lee CT, Urlaub H, Kastner B, Stark H, Lührmann R
Science 353 1399-1405 (2016)
PMID: 27562955
Related structures: EMD-4099

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 31-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142865 (preferred)
Entry contents:
27 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (31 distinct):
Pre-mRNA-splicing factor 8 Chain: A
Molecule details ›
Chain: A
Length: 2413 amino acids
Theoretical weight: 279.85 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: B
Molecule details ›
Chain: B
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 helicase BRR2 Chain: C
Molecule details ›
Chain: C
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 SLT11 Chain: D
Molecule details ›
Chain: D
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 BUD31 Chain: E
Molecule details ›
Chain: E
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: F
Molecule details ›
Chain: F
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 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
U2 snRNP component IST3 Chain: J
Molecule details ›
Chain: J
Length: 148 amino acids
Theoretical weight: 17.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40565 (Residues: 1-148; Coverage: 100%)
Gene names: IST3, SNU17, YIB5W, YIR005W
Sequence domains: RNA recognition motif
Pre-mRNA-splicing factor PRP46 Chain: K
Molecule details ›
Chain: K
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-splicing factor CWC26 Chain: L
Molecule details ›
Chain: L
Length: 266 amino acids
Theoretical weight: 30.53 KDa
Source organism: Saccharomyces cerevisiae
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-processing protein 45 Chain: M
Molecule details ›
Chain: M
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 leakage protein 1 Chain: N
Molecule details ›
Chain: N
Length: 204 amino acids
Theoretical weight: 23.69 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q07930 (Residues: 1-204; Coverage: 100%)
Gene names: L1591, PML1, YLR016C
Sequence domains: FHA domain
Pre-mRNA-splicing factor ATP-dependent RNA helicase-like protein PRP2 Chain: O
Molecule details ›
Chain: O
Length: 876 amino acids
Theoretical weight: 99.95 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P20095 (Residues: 1-876; Coverage: 100%)
Gene names: N2048, PRP2, RNA2, YNR011C
Sequence domains:
Pre-mRNA-splicing factor SYF1 Chain: P
Molecule details ›
Chain: P
Length: 859 amino acids
Theoretical weight: 100.34 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04048 (Residues: 1-859; Coverage: 100%)
Gene names: NTC90, SYF1, YDR416W
U2 snRNP component HSH155 Chain: Q
Molecule details ›
Chain: Q
Length: 971 amino acids
Theoretical weight: 110.17 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49955 (Residues: 1-971; Coverage: 100%)
Gene names: HSH155, YM8021.14, YMR288W
Pre-mRNA-splicing factor CLF1 Chain: R
Molecule details ›
Chain: R
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: HAT (Half-A-TPR) repeat
Pre-mRNA-splicing factor CEF1 Chain: W
Molecule details ›
Chain: W
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 RSE1 Chain: X
Molecule details ›
Chain: X
Length: 1361 amino acids
Theoretical weight: 153.96 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04693 (Residues: 1-1361; Coverage: 100%)
Gene names: RSE1, SAP130, YM9827.03C, YML049C
Sequence domains:
Pre-mRNA-splicing factor RDS3 Chain: Y
Molecule details ›
Chain: Y
Length: 107 amino acids
Theoretical weight: 12.28 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06835 (Residues: 1-107; Coverage: 100%)
Gene names: P9513.2, RDS3, YPR094W
Sequence domains: PHF5-like protein
RDS3 complex subunit 10 Chain: Z
Molecule details ›
Chain: Z
Length: 85 amino acids
Theoretical weight: 10.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C074 (Residues: 1-85; Coverage: 100%)
Gene names: RCP10, YNL138W-A, YSF3
Sequence domains: Splicing factor 3B subunit 10 (SF3b10)
Small nuclear ribonucleoprotein-associated protein B Chain: b
Molecule details ›
Chain: b
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 Chain: d
Molecule details ›
Chain: d
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 Chain: e
Molecule details ›
Chain: e
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 Chain: f
Molecule details ›
Chain: f
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 Chain: g
Molecule details ›
Chain: g
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 Chain: h
Molecule details ›
Chain: h
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 Chain: j
Molecule details ›
Chain: j
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
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: 179 nucleotides
Theoretical weight: 57.44 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
actin pre-mRNA Chain: 9
Molecule details ›
Chain: 9
Length: 572 nucleotides
Theoretical weight: 182.57 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.8Å
Relevant EMDB volumes: EMD-4099
Expression system: Escherichia coli

Quick links

Citations

35 review citations

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

10 mentions without citation

The life of U6 small nuclear RNA, from cradle to grave.
Didychuk et al. (2018)
9 more