7MCA

Structure of the S. cerevisiae origin recognition complex bound to the replication initiator Cdc6 and the ARS1 origin DNA.

  • Classification: REPLICATION
  • Organism(s): Saccharomyces cerevisiae
  • Expression System: unidentified baculovirus
  • Mutation(s): No 

  • Deposited: 2021-04-01 Released: 2021-06-02 
  • Deposition Author(s): Feng, X., Li, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The structure of ORC-Cdc6 on an origin DNA reveals the mechanism of ORC activation by the replication initiator Cdc6.

Feng, X., Noguchi, Y., Barbon, M., Stillman, B., Speck, C., Li, H.

(2021) Nat Commun 12: 3883-3883

  • DOI: 10.1038/s41467-021-24199-1
  • Primary Citation of Related Structures:  
    7MCA

  • PubMed Abstract: 

    • The Origin Recognition Complex (ORC) binds to sites in chromosomes to specify the location of origins of DNA replication. The S. cerevisiae ORC binds to specific DNA sequences throughout the cell cycle but becomes active only when it binds to the replication initiator Cdc6 ...

    The Origin Recognition Complex (ORC) binds to sites in chromosomes to specify the location of origins of DNA replication. The S. cerevisiae ORC binds to specific DNA sequences throughout the cell cycle but becomes active only when it binds to the replication initiator Cdc6. It has been unclear at the molecular level how Cdc6 activates ORC, converting it to an active recruiter of the Mcm2-7 hexamer, the core of the replicative helicase. Here we report the cryo-EM structure at 3.3 Å resolution of the yeast ORC-Cdc6 bound to an 85-bp ARS1 origin DNA. The structure reveals that Cdc6 contributes to origin DNA recognition via its winged helix domain (WHD) and its initiator-specific motif. Cdc6 binding rearranges a short α-helix in the Orc1 AAA+ domain and the Orc2 WHD, leading to the activation of the Cdc6 ATPase and the formation of the three sites for the recruitment of Mcm2-7, none of which are present in ORC alone. The results illuminate the molecular mechanism of a critical biochemical step in the licensing of eukaryotic replication origins.

    Organizational Affiliation: 

    Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA. Huilin.Li@vai.org.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 1A914Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC1
UniProt
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P54784
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UniProt GroupP54784
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 2B620Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC2
UniProt
Find proteins for P32833 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 3C616Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC
UniProt
Find proteins for P54790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 4D529Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC4, YPR162C, P9325.5
UniProt
Find proteins for P54791 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 5E479Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC5, YNL261W, N0834
UniProt
Find proteins for P50874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Origin recognition complex subunit 6F435Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC6, AAP1, YHR118C
UniProt
Find proteins for P38826 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 6I513Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC6, YJL194W, J0347
UniProt
Find proteins for P09119 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (85-MER)G85Saccharomyces cerevisiae
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (85-MER)H85Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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 StatesGM131754
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM45436
Biotechnology and Biological Sciences Research Council (BBSRC)United StatesBB/S001387.1
Biotechnology and Biological Sciences Research Council (BBSRC)United StatesBB/N000323/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-08-04
    Changes: Database references