5V8F

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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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: 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 inter ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM2 2868Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM2YBL023CYBL0438
EC: 3.6.4.12
Find proteins for P29469 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM3 3971Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM3YEL032WSYGP-ORF23
EC: 3.6.4.12
Find proteins for P24279 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM4 4933Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM4CDC54HCD21YPR019WYP9531.13
EC: 3.6.4.12
Find proteins for P30665 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Minichromosome maintenance protein 5 5775Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM5CDC46YLR274WL9328.1
EC: 3.6.4.12
Find proteins for P29496 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM6 61017Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM6YGL201C
EC: 3.6.4.12
Find proteins for P53091 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA replication licensing factor MCM7 7800Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MCM7CDC47YBR202WYBR1441
EC: 3.6.4.12
Find proteins for P38132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division cycle protein CDT1 8604Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TAH11CDT1SID2YJR046WJ1641
Find proteins for P47112 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 6 9513Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC6YJL194WJ0347
Find proteins for P09119 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 1 A913Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC1YML065W
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 2 B620Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC2RRR1SIR5YBR060CYBR0523
Find proteins for P32833 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 3 C616Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC3OAF1OIF1YLL004WL1365
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 5 E479Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC5YNL261WN0834
Find proteins for P50874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 4 D529Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC4YPR162CP9325.5
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 6 F435Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ORC6AAP1YHR118C
Find proteins for P38826 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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Entity ID: 15
MoleculeChainsLengthOrganismImage
DNA (39-MER)M39synthetic construct
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Entity ID: 16
MoleculeChainsLengthOrganismImage
DNA (39-MER)N39synthetic construct
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 

  • 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