2QBY

Crystal structure of a heterodimer of Cdc6/Orc1 initiators bound to origin DNA (from S. solfataricus)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex.

Dueber, E.L.Corn, J.E.Bell, S.D.Berger, J.M.

(2007) Science 317: 1210-1213

  • DOI: https://doi.org/10.1126/science.1143690
  • Primary Citation of Related Structures:  
    2QBY

  • PubMed Abstract: 

    The faithful duplication of genetic material depends on essential DNA replication initiation factors. Cellular initiators form higher-order assemblies on replication origins, using adenosine triphosphate (ATP) to locally remodel duplex DNA and facilitate proper loading of synthetic replisomal components. To better understand initiator function, we determined the 3.4 angstrom-resolution structure of an archaeal Cdc6/Orc1 heterodimer bound to origin DNA. The structure demonstrates that, in addition to conventional DNA binding elements, initiators use their AAA+ ATPase domains to recognize origin DNA. Together these interactions establish the polarity of initiator assembly on the origin and induce substantial distortions into origin DNA strands. Biochemical and comparative analyses indicate that AAA+/DNA contacts observed in the structure are dynamic and evolutionarily conserved, suggesting that the complex forms a core component of the basal initiation machinery.


  • Organizational Affiliation

    Miller Institute for Basic Research in Science, 2536 Channing Way 5190, University of California, Berkeley, CA 94720, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 6 homolog 1C [auth A]386Saccharolobus solfataricusMutation(s): 0 
Gene Names: cdc6-1
UniProt
Find proteins for Q980N4 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q980N4 
Go to UniProtKB:  Q980N4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ980N4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 6 homolog 3D [auth B]384Saccharolobus solfataricusMutation(s): 0 
Gene Names: cdc6-3
UniProt
Find proteins for Q97WM8 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97WM8 
Go to UniProtKB:  Q97WM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ97WM8
Sequence Annotations
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  • Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (33-MER)A [auth C]33N/A
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (33-MER)B [auth D]33N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

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I [auth A],
K [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
SPD
Query on SPD

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E [auth C],
F [auth C]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
K
Query on K

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G [auth D]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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H [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.649α = 90
b = 199.143β = 90
c = 213.405γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MLPHAREphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description