Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 57458.54 
• Atom Count: 3943 
• Residue Count: 431 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

2V1U

STRUCTURE OF THE AEROPYRUM PERNIX ORC1 PROTEIN IN COMPLEX WITH DNA

• DOI: 10.2210/pdb2V1U/pdb
• NDB: NA0305

• Classification: REPLICATION
• Organism(s): Aeropyrum pernix, Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)


• 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: 3.1 Å
• R-Value Free: 0.297 
• R-Value Work: 0.254 

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: 10.1126/science.1143664


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CELL DIVISION CONTROL PROTEIN 6 HOMOLOG	A	387	Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)	Mutation(s): 0  Gene Names: orc1
Find proteins for Q9YEV6 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Go to UniProtKB:  Q9YEV6

Entity ID: 2
Molecule	Chains	Length	Organism
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
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 & Interactions
ADP	A	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.1 Å
• R-Value Free: 0.297 
• R-Value Work: 0.254 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 75.700	α = 90.00
b = 75.700	β = 90.00
c = 395.110	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-30 
• 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
  Type: Advisory, Version format compliance