Skip to main content

 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

Validation slider image for 9BCX

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 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.

Macromolecule Content 

  • Total Structure Weight: 1,173.13 kDa 
  • Atom Count: 57,494 
  • Modeled Residue Count: 7,165 
  • Deposited Residue Count: 10,197 
  • Unique protein chains: 14
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2]868Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM2, YBL023C, YBL0438
EC: 3.6.4.12
UniProt
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29469 
Go to UniProtKB:  P29469
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29469
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]971Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM3, GI527_G0001749
EC: 3.6.4.12
UniProt
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P24279 
Go to UniProtKB:  P24279
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24279
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM5C [auth 5]775Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM5, GI527_G0004088
EC: 3.6.4.12
UniProt
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29496 
Go to UniProtKB:  P29496
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29496
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4D [auth 4]933Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM4, GI527_G0006071
EC: 3.6.4.12
UniProt
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P30665 
Go to UniProtKB:  P30665
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30665
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6E [auth 6]1,017Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM6, YGL201C
EC: 3.6.4.12
UniProt
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53091 
Go to UniProtKB:  P53091
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53091
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]845Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: MCM7, CDC47, YBR202W, YBR1441
EC: 3.6.4.12
UniProt
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38132 
Go to UniProtKB:  P38132
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38132
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 1G [auth B]914Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC1
UniProt
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54784 
Go to UniProtKB:  P54784
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54784
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 2H [auth C]620Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC2
UniProt
Find proteins for P32833 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32833 
Go to UniProtKB:  P32833
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32833
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 3I [auth D]616Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC
UniProt
Find proteins for P54790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54790 
Go to UniProtKB:  P54790
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54790
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 4J [auth E]529Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC4, YPR162C, P9325.5
UniProt
Find proteins for P54791 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P54791 
Go to UniProtKB:  P54791
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54791
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 5K [auth F]479Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC5, YNL261W, N0834
UniProt
Find proteins for P50874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50874 
Go to UniProtKB:  P50874
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50874
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 6L [auth G]435Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC6, AAP1, YHR118C
UniProt
Find proteins for P38826 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38826 
Go to UniProtKB:  P38826
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38826
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell division control protein 6M [auth I]513Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC6, YJL194W, J0347
UniProt
Find proteins for P09119 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P09119 
Go to UniProtKB:  P09119
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09119
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
TAH11 isoform 1N [auth 8]604Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TAH11, GI527_G0003298
UniProt
Find proteins for P47112 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47112 
Go to UniProtKB:  P47112
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47112
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 15
MoleculeChains LengthOrganismImage
DNA (39-MER)39synthetic construct
Sequence Annotations
Expand
Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (39-MER)39synthetic construct
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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