2V1U | pdb_00002v1u

STRUCTURE OF THE AEROPYRUM PERNIX ORC1 PROTEIN IN COMPLEX WITH DNA

• PDB DOI: https://doi.org/10.2210/pdb2V1U/pdb
• NAKB: 2V1U

• Classification: REPLICATION
• Organism(s): Aeropyrum pernix
• Mutation(s): No 


• Deposited: 2007-05-30 Released: 2007-09-18 
• Deposition Author(s): Gaudier, M., Schuwirth, B.S., Westcott, S.L., Wigley, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.297 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.255 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

Structural Basis of DNA Replication Origin Recognition by an Orc Protein.

Gaudier, M., Schuwirth, B.S., Westcott, S.L., Wigley, D.B.

(2007) Science 317: 1213

• PubMed: 17761880 
• DOI: https://doi.org/10.1126/science.1143664
• Primary Citation Related Structures: 
  2V1U


• PubMed Abstract: 
  

  DNA replication in archaea and in eukaryotes share many similarities. We report the structure of an archaeal origin recognition complex protein, ORC1, bound to an origin recognition box, a DNA sequence that is found in multiple copies at replication origins. DNA binding is mediated principally by a C-terminal winged helix domain that inserts deeply into the major and minor grooves, widening them both. However, additional DNA contacts are made with the N-terminal AAA+ domain, which inserts into the minor groove at a characteristic G-rich sequence, inducing a 35 degrees bend in the duplex and providing directionality to the binding site. Both contact regions also induce substantial unwinding of the DNA. The structure provides insight into the initial step in assembly of a replication origin and recruitment of minichromosome maintenance (MCM) helicase to that origin.

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 57.46 kDa 
• Atom Count: 3,951 
• Modeled Residue Count: 426 
• Deposited Residue Count: 431 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION CONTROL PROTEIN 6 HOMOLOG	A	387	Aeropyrum pernix	Mutation(s): 0
UniProt
Find proteins for Q9YEV6 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YEV6  Go to UniProtKB:  Q9YEV6

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*TP*CP*CP*AP*CP*AP*GP*GP *AP*AP*AP*CP*GP*GP*AP*GP*GP*GP*GP*T)-3'	B	22	Aeropyrum pernix

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*CP*CP*CP*TP*CP*CP*GP*TP *TP*TP*CP*CP*TP*GP*TP*GP*GP*AP*GP*A)-3'	C	22	Aeropyrum pernix

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.297 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.255 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.7	α = 90
b = 75.7	β = 90
c = 395.11	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
autoSHARP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-18 
Deposition Author(s): Gaudier, M., Schuwirth, B.S., Westcott, S.L., Wigley, D.B.

Revision History  

• Version 1.0: 2007-09-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other