9BCX | pdb_00009bcx

Cryo-EM structure of the S. cerevisiae ORC-Cdc6-Mcm2-7-DNA complex with a fully closed Mcm2-Mcm5 DNA entry gate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

MCM2-7 ring closure involves the Mcm5 C-terminus and triggers Mcm4 ATP hydrolysis.

Faull, S.V.Barbon, M.Mossler, A.Yuan, Z.Bai, L.Reuter, L.M.Riera, A.Winkler, C.Magdalou, I.Peach, M.Li, H.Speck, C.

(2025) Nat Commun 16: 14-14

  • DOI: https://doi.org/10.1038/s41467-024-55479-1
  • Primary Citation of Related Structures:  
    9BCX

  • PubMed Abstract: 

    The eukaryotic helicase MCM2-7, is loaded by ORC, Cdc6 and Cdt1 as a double-hexamer onto replication origins. The insertion of DNA into the helicase leads to partial MCM2-7 ring closure, while ATP hydrolysis is essential for consecutive steps in pre-replicative complex (pre-RC) assembly. Currently it is unknown how MCM2-7 ring closure and ATP-hydrolysis are controlled. A cryo-EM structure of an ORC-Cdc6-Cdt1-MCM2-7 intermediate shows a remodelled, fully-closed Mcm2/Mcm5 interface. The Mcm5 C-terminus (C5) contacts Orc3 and specifically recognises this closed ring. Interestingly, we found that normal helicase loading triggers Mcm4 ATP-hydrolysis, which in turn leads to reorganisation of the MCM2-7 complex and Cdt1 release. However, defective MCM2-7 ring closure, due to mutations at the Mcm2/Mcm5 interface, leads to MCM2-7 ring splitting and complex disassembly. As such we identify Mcm4 as the key ATPase in regulating pre-RC formation. Crucially, a stable Mcm2/Mcm5 interface is essential for productive ATP-hydrolysis-dependent remodelling of the helicase.


  • Organizational Affiliation
    • DNA Replication Group, Institute of Clinical Science, Imperial College London, 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: MCM2YBL023CYBL0438
EC: 3.6.4.12
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]971Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3GI527_G0001749
EC: 3.6.4.12
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM5C [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM5GI527_G0004088
EC: 3.6.4.12
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4D [auth 4]933Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM4GI527_G0006071
EC: 3.6.4.12
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6]1,017Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM6YGL201C
EC: 3.6.4.12
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 1G [auth B]914Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC1
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 2H [auth C]620Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC2
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 3I [auth D]616Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 4J [auth E]529Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC4YPR162CP9325.5
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 5K [auth F]479Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC5YNL261WN0834
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 6L [auth G]435Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC6AAP1YHR118C
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 6M [auth I]513Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC6YJL194WJ0347
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
TAH11 isoform 1N [auth 8]604Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TAH11GI527_G0003298
UniProt
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Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (39-MER)39synthetic construct
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Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (39-MER)39synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110387
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131754
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S001387/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/N000323/1
Wellcome TrustUnited Kingdom107903/Z/15/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-01
    Type: Initial release
  • Version 1.1: 2025-01-15
    Changes: Data collection, Database references