6HV9

S. cerevisiae CMG-Pol epsilon-DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of DNA-CMG-Pol epsilon elucidates the roles of the non-catalytic polymerase modules in the eukaryotic replisome.

Goswami, P.Abid Ali, F.Douglas, M.E.Locke, J.Purkiss, A.Janska, A.Eickhoff, P.Early, A.Nans, A.Cheung, A.M.C.Diffley, J.F.X.Costa, A.

(2018) Nat Commun 9: 5061-5061

  • DOI: 10.1038/s41467-018-07417-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Eukaryotic origin firing depends on assembly of the Cdc45-MCM-GINS (CMG) helicase. A key step is the recruitment of GINS that requires the leading-strand polymerase Pol epsilon, composed of Pol2, Dpb2, Dpb3, Dpb4. While a truncation of the catalytic ...

    Eukaryotic origin firing depends on assembly of the Cdc45-MCM-GINS (CMG) helicase. A key step is the recruitment of GINS that requires the leading-strand polymerase Pol epsilon, composed of Pol2, Dpb2, Dpb3, Dpb4. While a truncation of the catalytic N-terminal Pol2 supports cell division, Dpb2 and C-terminal Pol2 (C-Pol2) are essential for viability. Dpb2 and C-Pol2 are non-catalytic modules, shown or predicted to be related to an exonuclease and DNA polymerase, respectively. Here, we present the cryo-EM structure of the isolated C-Pol2/Dpb2 heterodimer, revealing that C-Pol2 contains a DNA polymerase fold. We also present the structure of CMG/C-Pol2/Dpb2 on a DNA fork, and find that polymerase binding changes both the helicase structure and fork-junction engagement. Inter-subunit contacts that keep the helicase-polymerase complex together explain several cellular phenotypes. At least some of these contacts are preserved during Pol epsilon-dependent CMG assembly on path to origin firing, as observed with DNA replication reconstituted in vitro.


    Organizational Affiliation

    Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck College, London, WC1E 7HX, UK.,Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. alessandro.costa@crick.ac.uk.,Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM3
3
971Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM3
EC: 3.6.4.12
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM3
Go to UniProtKB:  P24279
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM4
4
933Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM4 (CDC54, HCD21)
EC: 3.6.4.12
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM4
Go to UniProtKB:  P30665
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Minichromosome maintenance protein 5
5
775Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM5 (CDC46)
EC: 3.6.4.12
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM5
Go to UniProtKB:  P29496
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM6
6
1017Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM6
EC: 3.6.4.12
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM6
Go to UniProtKB:  P53091
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM2
2
868Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM2
EC: 3.6.4.12
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM2
Go to UniProtKB:  P29469
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA replication licensing factor MCM7
7
845Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MCM7 (CDC47)
EC: 3.6.4.12
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: MCM7
Go to UniProtKB:  P38132
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA replication complex GINS protein PSF1
C
208Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PSF1
Find proteins for Q12488 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12488
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA replication complex GINS protein PSF2
D
213Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PSF2
Find proteins for P40359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40359
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA replication complex GINS protein PSF3
E
194Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PSF3
Find proteins for Q12146 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12146
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA replication complex GINS protein SLD5
F
294Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SLD5
Find proteins for Q03406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03406
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Cell division control protein 45
G
650Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CDC45 (SLD4)
Find proteins for Q08032 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: CDC45
Go to UniProtKB:  Q08032
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase epsilon subunit B
B
689Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: DPB2
Find proteins for P24482 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P24482
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase epsilon catalytic subunit A
A
914Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: POL2 (DUN2)
EC: 2.7.7.7
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21951
Entity ID: 12
MoleculeChainsLengthOrganism
DNA/RNA (5'-R(*GP*CP*AP*GP*CP*CP*AP*CP*GP*C)-D(P*T)-R(P*GP*GP*CP*CP*G)-D(P*TP*TP*TP*T)-R(P*A)-3')X21Saccharomyces cerevisiae
Entity ID: 13
MoleculeChainsLengthOrganism
DNA/RNA (5'-D(P*T)-R(P*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*GP*CP*G)-D(P*T)-R(P*GP*GP*C)-D(P*T)-R(P*GP*C)-3')Y21Saccharomyces cerevisiae
Entity ID: 14
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')J7Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
AGS
Query on AGS

Download SDF File 
Download CCD File 
5
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--
Medical Research Council (United Kingdom)United Kingdom--
Cancer Research UKUnited Kingdom--

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release