6HV9

S. cerevisiae CMG-Pol epsilon-DNA


Experimental Data Snapshot

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

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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:  
    6HV9, 6HV8

  • 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-te ...

    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. alessandro.costa@crick.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3 3971Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4 4933Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
EC: 3.6.4.12
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5 5775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM5CDC46YLR274WL9328.1
EC: 3.6.4.12
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6 61017Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM6YGL201C
EC: 3.6.4.12
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2 2868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM2YBL023CYBL0438
EC: 3.6.4.12
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7 7845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1 C208Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF1YDR013WPZA208YD8119.18
Find proteins for Q12488 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2 D213Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF2YJL072CHRF213J1086
Find proteins for P40359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3 E194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF3YOL146W
Find proteins for Q12146 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5 F294Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLD5YDR489W
Find proteins for Q03406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 45 G650Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC45SLD4YLR103CL8004.11
Find proteins for Q08032 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit B B689Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.7
Find proteins for P24482 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit A A914Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL2DUN2YNL262WN0825
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for P21951 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 12
MoleculeChainsLengthOrganismImage
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
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Entity ID: 13
MoleculeChainsLengthOrganismImage
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
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 14
    MoleculeChainsLengthOrganismImage
    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
    AGS
    Query on AGS

    Download Ideal Coordinates CCD File 
    5
    PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
    C10 H16 N5 O12 P3 S
    NLTUCYMLOPLUHL-KQYNXXCUSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    A
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    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 

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