1FNN | pdb_00001fnn

CRYSTAL STRUCTURE OF CDC6P FROM PYROBACULUM AEROPHILUM

• PDB DOI: https://doi.org/10.2210/pdb1FNN/pdb

• Classification: CELL CYCLE
• Organism(s): Pyrobaculum aerophilum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-08-22 Released: 2000-10-04 
• Deposition Author(s): Liu, J., Smith, C.L., DeRyckere, D., DeAngelis, K., Martin, G.S., Berger, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.257 (Depositor) 
• R-Value Work: 
  0.221 (Depositor), 0.210 (DCC) 

Literature

Structure and function of Cdc6/Cdc18: implications for origin recognition and checkpoint control.

Liu, J., Smith, C.L., DeRyckere, D., DeAngelis, K., Martin, G.S., Berger, J.M.

(2000) Mol Cell 6: 637-648

• PubMed: 11030343 
• DOI: https://doi.org/10.1016/s1097-2765(00)00062-9
• Primary Citation of Related Structures:  
  1FNN


• PubMed Abstract: 
  

  Cdc6/Cdc18 is a conserved and essential component of prereplication complexes. The 2.0 A crystal structure of an archaeal Cdc6 ortholog, in conjunction with a mutational analysis of the homologous Cdc18 protein from Schizosaccharomyces pombe, reveals novel aspects of Cdc6/Cdc18 function. Two domains of Cdc6 form an AAA+-type nucleotide binding fold that is observed bound to Mg.ADP. A third domain adopts a winged-helix fold similar to known DNA binding modules. Sequence comparisons show that the winged-helix domain is conserved in Orc1, and mutagenesis data demonstrate that this region of Cdc6/Cdc18 is required for function in vivo. Additional mutational analyses suggest that nucleotide binding and/or hydrolysis by Cdc6/Cdc18 is required not only for progression through S phase, but also for maintenance of checkpoint control during S phase.

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Organizational Affiliation: 

Department of Molecular and Cell Biology, University of California, Berkeley 94720, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 89.43 kDa 
• Atom Count: 6,471 
• Modelled Residue Count: 758 
• Deposited Residue Count: 778 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION CONTROL PROTEIN 6	A, B	389	Pyrobaculum aerophilum	Mutation(s): 0
UniProt
Find proteins for Q8ZYK1 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)) Explore Q8ZYK1  Go to UniProtKB:  Q8ZYK1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	D [auth A], F [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.257 (Depositor) 
• R-Value Work:  0.221 (Depositor), 0.210 (DCC) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.07	α = 90
b = 132.07	β = 90
c = 82.2	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-10-04 
Deposition Author(s): Liu, J., Smith, C.L., DeRyckere, D., DeAngelis, K., Martin, G.S., Berger, J.M.

Revision History  

• Version 1.0: 2000-10-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations