9GM5 | pdb_00009gm5

OCCM maturation intermediate stalled with an Arginine Finger mutation in Mcm5: Conformer 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Unidirectional MCM translocation away from ORC drives origin licensing.

Butryn, A.Greiwe, J.F.Costa, A.

(2025) Nat Commun 16: 782-782

  • DOI: https://doi.org/10.1038/s41467-025-56143-y
  • Primary Citation of Related Structures:  
    9GJP, 9GJW, 9GM5

  • PubMed Abstract: 

    The MCM motor of the eukaryotic replicative helicase is loaded as a double hexamer onto DNA by the Origin Recognition Complex (ORC), Cdc6, and Cdt1. ATP binding supports formation of the ORC-Cdc6-Cdt1-MCM (OCCM) helicase-recruitment complex where ORC-Cdc6 and one MCM hexamer form two juxtaposed rings around duplex DNA. ATP hydrolysis by MCM completes MCM loading but the mechanism is unknown. Here, we used cryo-EM to characterise helicase loading with ATPase-dead Arginine Finger variants of the six MCM subunits. We report the structure of two MCM complexes with different DNA grips, stalled as they mature to loaded MCM. The Mcm2 Arginine Finger-variant stabilises DNA binding by Mcm2 away from ORC/Cdc6. The Arginine Finger-variant of the neighbouring Mcm5 subunit stabilises DNA engagement by Mcm5 downstream of the Mcm2 binding site. Cdc6 and Orc1 progressively disengage from ORC as MCM translocates along DNA. We observe that duplex DNA translocation by MCM involves a set of leading-strand contacts by the pre-sensor 1 ATPase hairpins and lagging-strand contacts by the helix-2-insert hairpins. Mutating any of the MCM residues involved impairs high-salt resistant DNA binding in vitro and double-hexamer formation assessed by electron microscopy. Thus, ATPase-powered duplex DNA translocation away from ORC underlies MCM loading.


  • Organizational Affiliation

    Macromolecular Machines Laboratory, The Francis Crick Institute, London, NW1 1AT, 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
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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
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5D [auth 5]775Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: MCM5CDC46YLR274WL9328.1
EC: 3.6.4.12
UniProt
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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
Cell division cycle protein CDT1G [auth 8]604Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TAH11CDT1SID2YJR046WJ1641
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 1H [auth A]949Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC1YML065W
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 2I [auth B]560Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC2RRR1SIR5YBR060CYBR0523
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 3J [auth C]616Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC3OAF1OIF1YLL004WL1365
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 4K [auth D]529Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC4YPR162CP9325.5
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 5L [auth E]479Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC5YNL261WN0834
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 6M [auth F]435Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC6AAP1YHR118C
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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Y [auth D],
Z [auth E]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

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P [auth 2],
R [auth 4],
T [auth 5],
V [auth 6]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

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Q [auth 2],
S [auth 4],
U [auth 5],
W [auth 6],
X [auth 7]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union820102
The Francis Crick InstituteUnited KingdomCC2009

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release