6RQC

Cryo-EM structure of an MCM loading intermediate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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

Mechanism of head-to-head MCM double-hexamer formation revealed by cryo-EM.

Miller, T.C.R.Locke, J.Greiwe, J.F.Diffley, J.F.X.Costa, A.

(2019) Nature 575: 704-710

  • DOI: 10.1038/s41586-019-1768-0
  • Primary Citation of Related Structures:  
    6RQC

  • PubMed Abstract: 
  • In preparation for bidirectional DNA replication, the origin recognition complex (ORC) loads two hexameric MCM helicases to form a head-to-head double hexamer around DNA 1,2 . The mechanism of MCM double-hexamer formation is debated. Single-molecule experiments have suggested a sequential mechanism, in which the ORC-dependent loading of the first hexamer drives the recruitment of the second hexamer 3 ...

    In preparation for bidirectional DNA replication, the origin recognition complex (ORC) loads two hexameric MCM helicases to form a head-to-head double hexamer around DNA 1,2 . The mechanism of MCM double-hexamer formation is debated. Single-molecule experiments have suggested a sequential mechanism, in which the ORC-dependent loading of the first hexamer drives the recruitment of the second hexamer 3 . By contrast, biochemical data have shown that two rings are loaded independently via the same ORC-mediated mechanism, at two inverted DNA sites 4,5 . Here we visualize MCM loading using time-resolved electron microscopy, and identify intermediates in the formation of the double hexamer. We confirm that both hexamers are recruited via the same interaction that occurs between ORC and the C-terminal domains of the MCM helicases. Moreover, we identify the mechanism of coupled MCM loading. The loading of the first MCM hexamer around DNA creates a distinct interaction site, which promotes the engagement of ORC at the N-terminal homodimerization interface of MCM. In this configuration, ORC is poised to direct the recruitment of the second hexamer in an inverted orientation, which is suitable for the formation of the double hexamer. Our results therefore reconcile the two apparently contrasting models derived from single-molecule experiments and biochemical data.


    Organizational Affiliation

    Macromolecular Machines Laboratory, Francis Crick Institute, London, UK. alessandro.costa@crick.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 1A949Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC1YML065W
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 2B620Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC2RRR1SIR5YBR060CYBR0523
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 3C616Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC3OAF1OIF1YLL004WL1365
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 4D529Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC4YPR162CP9325.5
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 5E479Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC5YNL261WN0834
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 6F435Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC6AAP1YHR118C
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2G [auth 2]868Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM2YBL023CYBL0438
EC: 3.6.4.12
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3H [auth 3]1006Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4I [auth 4]933Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
EC: 3.6.4.12
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5J [auth 5]775Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM5CDC46YLR274WL9328.1
EC: 3.6.4.12
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6K [auth 6]1017Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM6YGL201C
EC: 3.6.4.12
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7L [auth 7]845Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
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Entity ID: 13
MoleculeChainsLengthOrganismImage
DNA (88-MER)M [auth X]88Saccharomyces cerevisiae S288C
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Entity ID: 14
MoleculeChainsLengthOrganismImage
DNA (88-MER)N [auth Y]88Saccharomyces cerevisiae S288C
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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O [auth A],
Q [auth D],
S [auth E]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

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BA [auth 7],
U [auth 2],
W [auth 3],
Y [auth 5]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

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AA [auth 6],
CA [auth 7],
V [auth 2],
X [auth 4],
Z [auth 5]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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P [auth A],
R [auth D],
T [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited KingdomFC0010065
European Research CouncilUnited Kingdom820102

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Database references
  • Version 1.2: 2019-12-11
    Changes: Database references