7QHS

S. cerevisiae CMGE nucleating origin DNA melting


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

Mechanism of replication origin melting nucleated by CMG helicase assembly.

Lewis, J.S.Gross, M.H.Sousa, J.Henrikus, S.S.Greiwe, J.F.Nans, A.Diffley, J.F.X.Costa, A.

(2022) Nature 606: 1007-1014

  • DOI: https://doi.org/10.1038/s41586-022-04829-4
  • Primary Citation of Related Structures:  
    7QHS, 7Z13

  • PubMed Abstract: 

    The activation of eukaryotic origins of replication occurs in temporally separated steps to ensure that chromosomes are copied only once per cell cycle. First, the MCM helicase is loaded onto duplex DNA as an inactive double hexamer. Activation occurs after the recruitment of a set of firing factors that assemble two Cdc45-MCM-GINS (CMG) holo-helicases. CMG formation leads to the underwinding of DNA on the path to the establishment of the replication fork, but whether DNA becomes melted at this stage is unknown 1 . Here we use cryo-electron microscopy to image ATP-dependent CMG assembly on a chromatinized origin, reconstituted in vitro with purified yeast proteins. We find that CMG formation disrupts the double hexamer interface and thereby exposes duplex DNA in between the two CMGs. The two helicases remain tethered, which gives rise to a splayed dimer, with implications for origin activation and replisome integrity. Inside each MCM ring, the double helix becomes untwisted and base pairing is broken. This comes as the result of ATP-triggered conformational changes in MCM that involve DNA stretching and protein-mediated stabilization of three orphan bases. Mcm2 pore-loop residues that engage DNA in our structure are dispensable for double hexamer loading and CMG formation, but are essential to untwist the DNA and promote replication. Our results explain how ATP binding nucleates origin DNA melting by the CMG and maintains replisome stability at initiation.


  • Organizational Affiliation

    Macromolecular Machines Laboratory, The Francis Crick Institute, London, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2]868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS187PACBIOSEQ_LOCUS193PACBIOSEQ_LOCUS195PACBIOSEQ_LOCUS196SCNYR20_0007007400SCP684_0007007100
EC: 3.6.4.12
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]1,006Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4C [auth 4]933Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
EC: 3.6.4.12
UniProt
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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 MCM7E [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1F [auth H]208Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS944PACBIOSEQ_LOCUS956PACBIOSEQ_LOCUS958SCNYR20_0001022500SCP684_0001022000
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2G [auth I]213Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS3163PACBIOSEQ_LOCUS3191PACBIOSEQ_LOCUS3224PACBIOSEQ_LOCUS3231PACBIOSEQ_LOCUS3255SCNYR20_0009012300SCP684_0009011800
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3H [auth C]229Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PSF3YOL146W
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5I [auth D]294Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SLD5YDR489W
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 45J [auth E]657Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC45SLD4YLR103CL8004.11
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase epsilon subunit BK [auth F]689Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DPB2YPR175WP9705.7
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase epsilon catalytic subunit AL [auth G]2,222Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL2DUN2YNL262WN0825
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM5O [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PACBIOSEQ_LOCUS4112PACBIOSEQ_LOCUS4129PACBIOSEQ_LOCUS4153PACBIOSEQ_LOCUS4202SCNYR20_0004029000SCP684_0004028600
EC: 3.6.4.12
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Entity ID: 13
MoleculeChains LengthOrganismImage
DNA (26-MER)M [auth A]26DNA molecule
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Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (26-MER)N [auth B]26DNA molecule
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
CA [auth 5],
P [auth 2],
R [auth 3],
X [auth 7]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

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T [auth 4],
V [auth 6]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

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AA [auth G]
BA [auth G]
EA [auth 5]
Q [auth 2]
U [auth 4]
AA [auth G],
BA [auth G],
EA [auth 5],
Q [auth 2],
U [auth 4],
W [auth 6],
Z [auth 7]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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DA [auth 5],
S [auth 3],
Y [auth 7]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology Organization (EMBO)European Union211-2020
H2020 Marie Curie Actions of the European CommissionEuropean Union--
European Molecular Biology Organization (EMBO)European Union1177-2020
Human Frontier Science Program (HFSP)European UnionLT000834/2020-L
European Molecular Biology Organization (EMBO)European Union962-2019
The Francis Crick InstituteEuropean UnionFC001065
The Francis Crick InstituteEuropean UnionFC001066
Wellcome TrustEuropean Union106252/Z/14/Z
European Research Council (ERC)European Union669424-CHROMOREP
European Research Council (ERC)European Union820102

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-15
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references
  • Version 1.2: 2022-07-06
    Changes: Database references
  • Version 1.3: 2024-07-17
    Changes: Data collection, Refinement description