5V8F | pdb_00005v8f

Structural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.1 of the entry. See complete history. 


Literature

Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1.

Yuan, Z., Riera, A., Bai, L., Sun, J., Nandi, S., Spanos, C., Chen, Z.A., Barbon, M., Rappsilber, J., Stillman, B., Speck, C., Li, H.

(2017) Nat Struct Mol Biol 24: 316-324

  • DOI: https://doi.org/10.1038/nsmb.3372
  • Primary Citation of Related Structures:  
    5V8F

  • PubMed Abstract: 

    To initiate DNA replication, the origin recognition complex (ORC) and Cdc6 load an Mcm2-7 double hexamer onto DNA. Without ATP hydrolysis, ORC-Cdc6 recruits one Cdt1-bound Mcm2-7 hexamer, thus forming an ORC-Cdc6-Cdt1-Mcm2-7 (OCCM) helicase-loading intermediate. Here we report a 3.9-Å structure of Saccharomyces cerevisiae OCCM on DNA. Flexible Mcm2-7 winged-helix domains (WHDs) engage ORC-Cdc6. A three-domain Cdt1 configuration embraces Mcm2, Mcm4, and Mcm6, thus comprising nearly half of the hexamer. The Cdt1 C-terminal domain extends to the Mcm6 WHD, which binds the Orc4 WHD. DNA passes through the ORC-Cdc6 and Mcm2-7 rings. Origin DNA interaction is mediated by an α-helix within Orc4 and positively charged loops within Orc2 and Cdc6. The Mcm2-7 C-tier AAA+ ring is topologically closed by an Mcm5 loop that embraces Mcm2, but the N-tier-ring Mcm2-Mcm5 interface remains open. This structure suggests a loading mechanism of the first Cdt1-bound Mcm2-7 hexamer by ORC-Cdc6.

    • Organizational Affiliation: 

    Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, Michigan, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2A [auth 2]868Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM2, YBL023C, YBL0438
EC: 3.6.4.12
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3B [auth 3]971Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM3, YEL032W, SYGP-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 cerevisiae S288CMutation(s): 0 
Gene Names: MCM4, CDC54, HCD21, YPR019W, YP9531.13
EC: 3.6.4.12
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5D [auth 5]775Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM5, CDC46, YLR274W, L9328.1
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 cerevisiae S288CMutation(s): 0 
Gene Names: MCM6, YGL201C
EC: 3.6.4.12
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7F [auth 7]800Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM7, CDC47, YBR202W, YBR1441
EC: 3.6.4.12
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division cycle protein CDT1G [auth 8]604Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TAH11, CDT1, SID2, YJR046W, J1641
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 6H [auth 9]513Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC6, YJL194W, J0347
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 1I [auth A]913Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC1, YML065W
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 2J [auth B]620Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC2, RRR1, SIR5, YBR060C, YBR0523
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 3K [auth C]616Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC3, OAF1, OIF1, YLL004W, L1365
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 5L [auth E]479Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC5, YNL261W, N0834
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 4M [auth D]529Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC4, YPR162C, P9325.5
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 6N [auth F]435Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC6, AAP1, YHR118C
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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 StatesGM111742
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM45436
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomP56061
Wellcome TrustUnited KingdomP56628

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2017-11-08
    Changes: Derived calculations, Experimental preparation
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-04-22
    Type: Coordinate replacement
    Reason: Chirality error
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-10-09
    Changes: Data collection, Database references, Structure summary