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 6HV9 | pdb_00006hv9

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

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This is version 2.2 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: https://doi.org/10.1038/s41467-018-07417-1
  • Primary Citation Related Structures: 
    6HV8, 6HV9

  • 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 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: 
    • Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.

Macromolecule Content 

  • Total Structure Weight: 985.53 kDa 
  • Atom Count: 47,617 
  • Modeled Residue Count: 6,089 
  • Deposited Residue Count: 8,620 
  • Unique protein chains: 13
  • Unique nucleic acid chains: 3

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3A [auth 3]971Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3, YEL032W, SYGP-ORF23
EC: 3.6.4.12
UniProt
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP24279
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4B [auth 4]933Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM4, CDC54, HCD21, YPR019W, YP9531.13
EC: 3.6.4.12
UniProt
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM5C [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4112, PACBIOSEQ_LOCUS4129, PACBIOSEQ_LOCUS4153, PACBIOSEQ_LOCUS4202, SCNYR20_0004029000, SCP684_0004028600
EC: 3.6.4.12
UniProt
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP29496
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6D [auth 6]1,017Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM6, YGL201C
EC: 3.6.4.12
UniProt
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2E [auth 2]868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS187, PACBIOSEQ_LOCUS193, PACBIOSEQ_LOCUS195, PACBIOSEQ_LOCUS196, SCNYR20_0007007400, SCP684_0007007100
EC: 3.6.4.12
UniProt
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7, CDC47, YBR202W, YBR1441
EC: 3.6.4.12
UniProt
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1G [auth C]208Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS944, PACBIOSEQ_LOCUS956, PACBIOSEQ_LOCUS958, SCNYR20_0001022500, SCP684_0001022000
UniProt
Find proteins for Q12488 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ12488
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2H [auth D]213Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS3163, PACBIOSEQ_LOCUS3191, PACBIOSEQ_LOCUS3224, PACBIOSEQ_LOCUS3231, PACBIOSEQ_LOCUS3255, SCNYR20_0009012300, SCP684_0009011800
UniProt
Find proteins for P40359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40359
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3I [auth E]194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF3, GI527_G0005213
UniProt
Find proteins for Q12146 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5J [auth F]294Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLD5, YDR489W
UniProt
Find proteins for Q03406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ03406
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division control protein 45K [auth G]650Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC45, SLD4, YLR103C, L8004.11
UniProt
Find proteins for Q08032 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ08032
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit BO [auth B]689Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P24482 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunitP [auth A]914Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL2, GI527_G0004851
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 12
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*AP*GP*CP*CP*AP*CP*GP*CP*TP*GP*GP*CP*CP*GP*TP*TP*TP*TP*A)-3')L [auth X]21Saccharomyces cerevisiae
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Reference Sequence
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Entity ID: 13
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*AP*AP*AP*AP*CP*GP*GP*CP*CP*AP*GP*CP*GP*TP*GP*GP*CP*TP*GP*C)-3')M [auth Y]21Saccharomyces cerevisiae
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Reference Sequence
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')N [auth J]7Saccharomyces cerevisiae
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

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

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 2.0: 2023-07-05
    Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2025-10-01
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 2.2: 2025-12-17
    Changes: Data collection