7TJI

S. cerevisiae ORC bound to 84 bp ARS1 DNA and Cdc6 (state 2) with flexible Orc6 N-terminal domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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

A mechanism of origin licensing control through autoinhibition of S. cerevisiae ORC·DNA·Cdc6.

Schmidt, J.M.Yang, R.Kumar, A.Hunker, O.Seebacher, J.Bleichert, F.

(2022) Nat Commun 13: 1059-1059

  • DOI: https://doi.org/10.1038/s41467-022-28695-w
  • Primary Citation of Related Structures:  
    7TJF, 7TJH, 7TJI, 7TJJ, 7TJK

  • PubMed Abstract: 

    The coordinated action of multiple replicative helicase loading factors is needed for the licensing of replication origins prior to DNA replication. Binding of the Origin Recognition Complex (ORC) to DNA initiates the ATP-dependent recruitment of Cdc6, Cdt1 and Mcm2-7 loading, but the structural details for timely ATPase site regulation and for how loading can be impeded by inhibitory signals, such as cyclin-dependent kinase phosphorylation, are unknown. Using cryo-electron microscopy, we have determined several structures of S. cerevisiae ORC·DNA·Cdc6 intermediates at 2.5-2.7 Å resolution. These structures reveal distinct ring conformations of the initiator·co-loader assembly and inactive ATPase site configurations for ORC and Cdc6. The Orc6 N-terminal domain laterally engages the ORC·Cdc6 ring in a manner that is incompatible with productive Mcm2-7 docking, while deletion of this Orc6 region alleviates the CDK-mediated inhibition of Mcm7 recruitment. Our findings support a model in which Orc6 promotes the assembly of an autoinhibited ORC·DNA·Cdc6 intermediate to block origin licensing in response to CDK phosphorylation and to avert DNA re-replication.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Basel, 4058, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 1917Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC1YML065W
UniProt
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP54784
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 2620Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC2
UniProt
Find proteins for P32833 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP32833
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 3616Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC
UniProt
Find proteins for P54790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 4532Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC4YPR162CP9325.5
UniProt
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UniProt GroupP54791
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 5479Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC5YNL261WN0834
UniProt
Find proteins for P50874 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP50874
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Origin recognition complex subunit 6435Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: ORC6AAP1YHR118C
UniProt
Find proteins for P38826 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP38826
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 6516Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC6YJL194WJ0347
UniProt
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA, 84 bp ARS184Saccharomyces cerevisiae
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA, 84 bp ARS184Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
J [auth A],
L [auth D],
N [auth E],
P [auth I]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth A],
M [auth D],
O [auth E],
Q [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 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 StatesR01-GM141313
European Research Council (ERC)United StatesERC-STG-757909
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM008283

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-05
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Data collection