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 2.0 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: https://doi.org/10.1038/s41467-018-07417-1
  • Primary Citation of 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.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3A [auth 3]971Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
UniProt
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4B [auth 4]933Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
EC: 3.6.4.12
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM5C [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4112PACBIOSEQ_LOCUS4129PACBIOSEQ_LOCUS4153PACBIOSEQ_LOCUS4202SCNYR20_0004029000SCP684_0004028600
EC: 3.6.4.12
UniProt
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6D [auth 6]1,017Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM6YGL201C
EC: 3.6.4.12
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2E [auth 2]868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS187PACBIOSEQ_LOCUS193PACBIOSEQ_LOCUS195PACBIOSEQ_LOCUS196SCNYR20_0007007400SCP684_0007007100
EC: 3.6.4.12
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
UniProt
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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_LOCUS944PACBIOSEQ_LOCUS956PACBIOSEQ_LOCUS958SCNYR20_0001022500SCP684_0001022000
UniProt
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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_LOCUS3163PACBIOSEQ_LOCUS3191PACBIOSEQ_LOCUS3224PACBIOSEQ_LOCUS3231PACBIOSEQ_LOCUS3255SCNYR20_0009012300SCP684_0009011800
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3I [auth E]194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF3GI527_G0005213
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5J [auth F]294Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLD5YDR489W
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 45K [auth G]650Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC45SLD4YLR103CL8004.11
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit BO [auth B]689Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunitP [auth A]914Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL2GI527_G0004851
EC: 2.7.7.7
UniProt
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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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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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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')N [auth J]7Saccharomyces cerevisiae
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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