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Structure paper

TitleStructural basis for conformational equilibrium of the catalytic spliceosome.
Journal, issue, pagesMol Cell, Vol. 81, Issue 7, Page 1439-11452.e9, Year 2021
Publish dateApr 1, 2021
AuthorsMax E Wilkinson / Sebastian M Fica / Wojciech P Galej / Kiyoshi Nagai /
PubMed AbstractThe ATPase Prp16 governs equilibrium between the branching (B/C) and exon ligation (C/P) conformations of the spliceosome. Here, we present the electron cryomicroscopy reconstruction of the ...The ATPase Prp16 governs equilibrium between the branching (B/C) and exon ligation (C/P) conformations of the spliceosome. Here, we present the electron cryomicroscopy reconstruction of the Saccharomyces cerevisiae C-complex spliceosome at 2.8 Å resolution and identify a novel C-complex intermediate (C) that elucidates the molecular basis for this equilibrium. The exon-ligation factors Prp18 and Slu7 bind to C before ATP hydrolysis by Prp16 can destabilize the branching conformation. Biochemical assays suggest that these pre-bound factors prime the C complex for conversion to C by Prp16. A complete model of the Prp19 complex (NTC) reveals how the branching factors Yju2 and Isy1 are recruited by the NTC before branching. Prp16 remodels Yju2 binding after branching, allowing Yju2 to remain tethered to the NTC in the C complex to promote exon ligation. Our results explain how Prp16 action modulates the dynamic binding of step-specific factors to alternatively stabilize the C or C conformation and establish equilibrium of the catalytic spliceosome.
External linksMol Cell / PubMed:33705709 / PubMed Central
MethodsEM (single particle)
Resolution2.8 - 8.0 Å
Structure data

12106

7b9v

EMDB-12106: Yeast C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound, composite map
PDB-7b9v: Yeast C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-12107:
Yeast C complex spliceosome, focused refinement on core
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-12108:
Yeast C complex spliceosome, focused refinement on U2 snRNP
Method: EM (single particle) / Resolution: 3.58 Å

EMDB-12109:
Yeast C complex spliceosome, focused refinement on NTC
Method: EM (single particle) / Resolution: 3.82 Å

EMDB-12110:
Yeast C complex spliceosome, focused refinement on Brr2/Prp8-Jab1 and Prp16
Method: EM (single particle) / Resolution: 8.0 Å

EMDB-12111:
Yeast C complex spliceosome, focused refinement on just Brr2/Prp8-Jab1
Method: EM (single particle) / Resolution: 7.15 Å

EMDB-12112:
Yeast C complex spliceosome, overall map after focused classification on Prp17
Method: EM (single particle) / Resolution: 3.67 Å

EMDB-12113:
Yeast C complex spliceosome, overall map after focused classification on Slu7 zinc knuckle
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-12114:
Yeast C complex spliceosome, overall map after focused classification on Prp18
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-12115:
Yeast C complex spliceosome, reconstructed signal-subtracted map after focused classification on Prp19
Method: EM (single particle) / Resolution: 7.3 Å

EMDB-12116:
Yeast C complex spliceosome, overall map after focused classification on Prp19
Method: EM (single particle) / Resolution: 3.97 Å

EMDB-12117:
Yeast C complex spliceosome, overall map after focused classification on U5 Sm ring
Method: EM (single particle) / Resolution: 3.13 Å

EMDB-12118:
Yeast C complex spliceosome, overall map after focused classification on Cwc22 NTD
Method: EM (single particle) / Resolution: 3.16 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-KGN:
D-chiro inositol hexakisphosphate

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

ChemComp-ZN:
Unknown entry

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • Baker's yeast (brewer's yeast)
KeywordsSPLICING / spliceosome / RNA / ribozyme

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