7B9V

Yeast C complex spliceosome at 2.8 Angstrom resolution with Prp18/Slu7 bound


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for conformational equilibrium of the catalytic spliceosome.

Wilkinson, M.E.Fica, S.M.Galej, W.P.Nagai, K.

(2021) Mol Cell 81: 1439

  • DOI: https://doi.org/10.1016/j.molcel.2021.02.021
  • Primary Citation of Related Structures:  
    7B9V

  • PubMed Abstract: 

    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 i ) that elucidates the molecular basis for this equilibrium. The exon-ligation factors Prp18 and Slu7 bind to C i 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.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. Electronic address: mwilkin@mrc-lmb.cam.ac.uk.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 8D [auth A]2,413Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P33334 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing helicase BRR2E [auth B]2,163Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.13
UniProt
Find proteins for P32639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SNU114F [auth C]1,008Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor YJU2G [auth D]291Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC25I [auth F]179Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ISY1J [auth G]235Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
CWC22 isoform 1K [auth H]577Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
BJ4_G0054360.mRNA.1.CDS.1M [auth J]451Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing protein 45N [auth K]379Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
BUD31 isoform 1O [auth L]157Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC2P [auth M]339Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLT11Q [auth N]364Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Y55_G0042700.mRNA.1.CDS.1R [auth O]590Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC15S [auth P]175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16T [auth Q]1,071Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor CWC21U [auth R]135Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5PZG6 (Saccharomyces cerevisiae)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
CLF1 isoform 1V [auth S]687Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5PT67 (Saccharomyces cerevisiae)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
SYF1 isoform 1W [auth T]859Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
HLJ1_G0053790.mRNA.1.CDS.1X [auth W]238Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Unassigned structureY [auth X]240Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
BJ4_G0027490.mRNA.1.CDS.1Z [auth Y]111Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5Q318 (Saccharomyces cerevisiae)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
NTC20 isoform 1AA [auth Z]140Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor 18BA [auth a]251Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for A0A6A5PX22 (Saccharomyces cerevisiae)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein-associated protein BCA [auth b],
KA [auth k]
196Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40018 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SLU7DA [auth c]382Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D3EA [auth d],
NA [auth n]
101Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein EFA [auth e],
PA [auth p]
94Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein FGA [auth f],
QA [auth q]
86Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P54999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein GHA [auth g],
RA [auth r]
77Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D1IA [auth h],
LA [auth l]
146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Small nuclear ribonucleoprotein Sm D2JA [auth j],
MA [auth m]
110Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
CDC40 isoform 1OA [auth o]455Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
SNT309 isoform 1SA [auth s]175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-processing factor 19TA [auth t],
UA [auth u],
VA [auth v],
WA [auth w]
503Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.3.2.27
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Pre-mRNA-splicing factor SYF2XA [auth y]215Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
U2 snRNAA [auth 2]1,175Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChains LengthOrganismImage
U5 snRNAB [auth 5]214Saccharomyces cerevisiae
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Entity ID: 3
MoleculeChains LengthOrganismImage
U6 snRNAC [auth 6]112Saccharomyces cerevisiae
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Entity ID: 8
MoleculeChains LengthOrganismImage
5' exon of UBC4 mRNAH [auth E]47Saccharomyces cerevisiae
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Entity ID: 12
MoleculeChains LengthOrganismImage
Branched intron and 3' exon of UBC4 pre-mRNAL [auth I]95Saccharomyces cerevisiae
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KGN
Query on KGN

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EB [auth A]D-chiro inositol hexakisphosphate
C6 H18 O24 P6
IMQLKJBTEOYOSI-LKPKBOIGSA-N
GTP
Query on GTP

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GB [auth C]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

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HB [auth D]
IB [auth L]
JB [auth L]
KB [auth L]
LB [auth M]
HB [auth D],
IB [auth L],
JB [auth L],
KB [auth L],
LB [auth M],
MB [auth N],
NB [auth N],
OB [auth c]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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DB [auth 6]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth 6]
BB [auth 6]
CB [auth 6]
FB [auth C]
YA [auth 6]
AB [auth 6],
BB [auth 6],
CB [auth 6],
FB [auth C],
YA [auth 6],
ZA [auth 6]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
OA [auth o]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIXdev-3965
MODEL REFINEMENTISOLDE1.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)United KingdomSPLICE3D
Medical Research Council (MRC, United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2021-04-14
    Changes: Database references