8Q6O

X. laevis CMG dimer bound to dimeric DONSON - without ATPase

  • Classification: REPLICATION
  • Organism(s): Xenopus laevis
  • Mutation(s): No 

  • Deposited: 2023-08-14 Released: 2023-10-18 
  • Deposition Author(s): Butryn, A., Cvetkovic, M.A., Costa, A.
  • Funding Organization(s): The Francis Crick Institute, European Research Council (ERC), Marie Sklodowska-Curie Actions, FragNET ITN, Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structural mechanism of dimeric DONSON in replicative helicase activation.

Cvetkovic, M.A.Passaretti, P.Butryn, A.Reynolds-Winczura, A.Kingsley, G.Skagia, A.Fernandez-Cuesta, C.Poovathumkadavil, D.George, R.Chauhan, A.S.Jhujh, S.S.Stewart, G.S.Gambus, A.Costa, A.

(2023) Mol Cell 83: 4017

  • DOI: https://doi.org/10.1016/j.molcel.2023.09.029
  • Primary Citation of Related Structures:  
    8Q6O, 8Q6P

  • PubMed Abstract: 

    The MCM motor of the replicative helicase is loaded onto origin DNA as an inactive double hexamer before replication initiation. Recruitment of activators GINS and Cdc45 upon S-phase transition promotes the assembly of two active CMG helicases. Although work with yeast established the mechanism for origin activation, how CMG is formed in higher eukaryotes is poorly understood. Metazoan Downstream neighbor of Son (DONSON) has recently been shown to deliver GINS to MCM during CMG assembly. What impact this has on the MCM double hexamer is unknown. Here, we used cryoelectron microscopy (cryo-EM) on proteins isolated from replicating Xenopus egg extracts to identify a double CMG complex bridged by a DONSON dimer. We find that tethering elements mediating complex formation are essential for replication. DONSON reconfigures the MCM motors in the double CMG, and primordial dwarfism patients' mutations disrupting DONSON dimerization affect GINS and MCM engagement in human cells and DNA synthesis in Xenopus egg extracts.


  • Organizational Affiliation

    Macromolecular Machines Laboratory, The Francis Crick Institute, London NW1 1AT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor mcm2A,
R [auth 2]
886Xenopus laevisMutation(s): 0 
EC: 3.6.4.12
UniProt
Find proteins for P55861 (Xenopus laevis)
Explore P55861 
Go to UniProtKB:  P55861
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55861
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Maternal DNA replication licensing factor mcm3B,
S [auth 3]
807Xenopus laevisMutation(s): 0 
EC: 3.6.4.12
UniProt
Find proteins for P49739 (Xenopus laevis)
Explore P49739 
Go to UniProtKB:  P49739
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49739
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor mcm4-BC,
T [auth 4]
863Xenopus laevisMutation(s): 0 
EC: 3.6.4.12
UniProt
Find proteins for P30664 (Xenopus laevis)
Explore P30664 
Go to UniProtKB:  P30664
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30664
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor mcm5-AD,
U [auth 5]
735Xenopus laevisMutation(s): 0 
EC: 3.6.4.12
UniProt
Find proteins for P55862 (Xenopus laevis)
Explore P55862 
Go to UniProtKB:  P55862
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55862
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Maternal DNA replication licensing factor mcm6E,
V [auth 6]
821Xenopus laevisMutation(s): 0 
EC: 3.6.4.12
UniProt
Find proteins for Q5FWY4 (Xenopus laevis)
Explore Q5FWY4 
Go to UniProtKB:  Q5FWY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5FWY4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor mcm7-BF,
W [auth 7]
720Xenopus laevisMutation(s): 0 
EC: 3.6.4.12
UniProt
Find proteins for Q7ZXB1 (Xenopus laevis)
Explore Q7ZXB1 
Go to UniProtKB:  Q7ZXB1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ZXB1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF1G [auth M],
M [auth G]
196Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q7ZT47 (Xenopus laevis)
Explore Q7ZT47 
Go to UniProtKB:  Q7ZT47
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ZT47
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF2H [auth N],
O [auth H]
185Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q7ZT46 (Xenopus laevis)
Explore Q7ZT46 
Go to UniProtKB:  Q7ZT46
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ZT46
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein PSF3I [auth O],
P [auth I]
210Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q7ZT01 (Xenopus laevis)
Explore Q7ZT01 
Go to UniProtKB:  Q7ZT01
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ZT01
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 45 homologJ [auth P],
Q [auth J]
567Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q9YHZ6 (Xenopus laevis)
Explore Q9YHZ6 
Go to UniProtKB:  Q9YHZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YHZ6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication complex GINS protein SLD5K [auth Q],
N [auth K]
221Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q7ZT48 (Xenopus laevis)
Explore Q7ZT48 
Go to UniProtKB:  Q7ZT48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7ZT48
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Protein downstream neighbor of son homologL [auth R],
X [auth L]
579Xenopus laevisMutation(s): 0 
UniProt
Find proteins for Q5U4U4 (Xenopus laevis)
Explore Q5U4U4 
Go to UniProtKB:  Q5U4U4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5U4U4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth E]
CA [auth F]
DA [auth 2]
EA [auth 4]
AA [auth D],
BA [auth E],
CA [auth F],
DA [auth 2],
EA [auth 4],
FA [auth 5],
GA [auth 6],
HA [auth 7],
Y [auth A],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomFC001065
European Research Council (ERC)European Union820102
Marie Sklodowska-Curie Actions, FragNET ITNEuropean Union845939
Wellcome TrustUnited Kingdom215510/Z/19/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T001860/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-18
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Database references