Structure of the Aeropyrum Pernix ORC2 protein (ADP form)

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 

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Conformational Changes Induced by Nucleotide Binding in Cdc6/Orc from Aeropyrum Pernix

Singleton, M.R.Morales, R.Grainge, I.Cook, N.Isupov, M.N.Wigley, D.B.

(2004) J Mol Biol 343: 547

  • DOI: https://doi.org/10.1016/j.jmb.2004.08.044
  • Primary Citation of Related Structures:  
    1W5S, 1W5T

  • PubMed Abstract: 

    Archaea contain one or more proteins with homology to eukaryotic ORC/Cdc6 proteins. Sequence analysis suggests the existence of at least two subfamilies of these proteins, for which we propose the nomenclature ORC1 and ORC2. We have determined crystal structures of the ORC2 protein from the archaeon Aeropyrum pernix in complexes with ADP or a non-hydrolysable ATP analogue, ADPNP. Between two crystal forms, there are three crystallographically independent views of the ADP complex and two of the ADPNP complex. The protein molecules in the three complexes with ADP adopt very different conformations, while the two complexes with ADPNP are the same. These structures indicate that there is considerable conformational flexibility in ORC2 but that ATP binding stabilises a single conformation. We show that the ORC2 protein can bind DNA, and that this activity is associated with the C-terminal domain of the protein. We present a model for the interaction of the winged helix (WH) domain of ORC2 with DNA that differs from that proposed previously for Pyrobaculum aerophilum ORC/Cdc6.

  • Organizational Affiliation

    Cancer Research UK Clare Hall Laboratories, The London Research Institute, Blanche Lane, South Mimms, Potters Bar, Herts EN6 3LD, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
412Aeropyrum pernixMutation(s): 0 
Find proteins for Q9YFU8 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YFU8 
Go to UniProtKB:  Q9YFU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YFU8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.495α = 90
b = 101.911β = 90
c = 255.797γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance