6HV9 image
Deposition Date 2018-10-10
Release Date 2018-12-12
Last Version Date 2023-07-05
Entry Detail
PDB ID:
6HV9
Title:
S. cerevisiae CMG-Pol epsilon-DNA
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
4.98 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA replication licensing factor MCM2
Chain IDs:E (auth: 2)
Chain Length:868
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA replication licensing factor MCM3
Gene (Uniprot):MCM3
Chain IDs:A (auth: 3)
Chain Length:971
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA replication licensing factor MCM4
Gene (Uniprot):MCM4
Chain IDs:B (auth: 4)
Chain Length:933
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA replication licensing factor MCM5
Chain IDs:C (auth: 5)
Chain Length:775
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA replication licensing factor MCM6
Gene (Uniprot):MCM6
Chain IDs:D (auth: 6)
Chain Length:1017
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA replication licensing factor MCM7
Gene (Uniprot):MCM7
Chain IDs:F (auth: 7)
Chain Length:845
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA polymerase epsilon catalytic subunit
Chain IDs:P (auth: A)
Chain Length:914
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA polymerase epsilon subunit B
Gene (Uniprot):DPB2
Chain IDs:O (auth: B)
Chain Length:689
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA replication complex GINS protein PSF1
Chain IDs:G (auth: C)
Chain Length:208
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA replication complex GINS protein PSF2
Chain IDs:H (auth: D)
Chain Length:213
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA replication complex GINS protein PSF3
Chain IDs:I (auth: E)
Chain Length:194
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:DNA replication complex GINS protein SLD5
Gene (Uniprot):SLD5
Chain IDs:J (auth: F)
Chain Length:294
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Cell division control protein 45
Gene (Uniprot):CDC45
Chain IDs:K (auth: G)
Chain Length:650
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')
Chain IDs:N (auth: J)
Chain Length:7
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polydeoxyribonucleotide
Molecule: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')
Chain IDs:L (auth: X)
Chain Length:21
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polydeoxyribonucleotide
Molecule: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')
Chain IDs:M (auth: Y)
Chain Length:21
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Primary Citation
Structure of DNA-CMG-Pol epsilon elucidates the roles of the non-catalytic polymerase modules in the eukaryotic replisome.
Nat Commun 9 5061 5061 (2018)
PMID: 30498216 DOI: 10.1038/s41467-018-07417-1

Abstact

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.

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Primary Citation of related structures