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:  
    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 ...

    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 MCM3A [auth 3]971Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3, YEL032W, SYGP-ORF23
EC: 3.6.4.12
UniProt
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Entity ID: 2
MoleculeChainsSequence 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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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5C [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM5, CDC46, YLR274W, L9328.1
EC: 3.6.4.12
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6D [auth 6]1017Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM6, YGL201C
EC: 3.6.4.12
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2E [auth 2]868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM2, YBL023C, YBL0438
EC: 3.6.4.12
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7, CDC47, YBR202W, YBR1441
EC: 3.6.4.12
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1G [auth C]208Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF1, YDR013W, PZA208, YD8119.18
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2H [auth D]213Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF2, YJL072C, HRF213, J1086
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3I [auth E]194Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF3, YOL146W
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5J [auth F]294Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLD5, YDR489W
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 45K [auth G]650Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC45, SLD4, YLR103C, L8004.11
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit BO [auth B]689Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.7
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit AP [auth A]914Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL2, DUN2, YNL262W, N0825
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
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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')L [auth X]21Saccharomyces 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')M [auth Y]21Saccharomyces cerevisiae
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Entity ID: 14
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')N [auth J]7Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS
Query on AGS
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Q [auth 5],
R [auth 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 
S [auth A],
T [auth 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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View more in-depth experimental data

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