Biological Assembly 1  

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 129.87 kDa 
• Atom Count: 8,960 
• Modelled Residue Count: 1,017 
• Deposited Residue Count: 1,037 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 1RZ9

Crystal Structure of AAV Rep complexed with the Rep-binding sequence

• PDB DOI: 10.2210/pdb1RZ9/pdb
• NDB: PD0506

• Classification: Viral protein/DNA
• Organism(s): adeno-associated virus 5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-12-24 Released: 2004-02-17 
• Deposition Author(s): Hickman, A.B., Ronning, D.R., Perez, Z.N., Kotin, R.M., Dyda, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.315 
• R-Value Work: 0.286 
• R-Value Observed: 0.286 

Literature

The nuclease domain of adeno-associated virus rep coordinates replication initiation using two distinct DNA recognition interfaces.

Hickman, A.B., Ronning, D.R., Perez, Z.N., Kotin, R.M., Dyda, F.

(2004) Mol Cell 13: 403-414

• PubMed: 14967147 
• DOI: 10.1016/s1097-2765(04)00023-1
• Primary Citation of Related Structures:  
  1RZ9, 1UUT


• PubMed Abstract: 
  

Integration into a particular location in human chromosomes is a unique property of the adeno-associated virus (AAV). This reaction requires the viral Rep protein and AAV origin sequences. To understand how Rep recognizes DNA, we have determined the structures of the Rep endonuclease domain separately complexed with two DNA substrates: the Rep binding site within the viral inverted terminal repeat and one of the terminal hairpin arms. At the Rep binding site, five Rep monomers bind five tetranucleotide direct repeats; each repeat is recognized by two Rep monomers from opposing faces of the DNA. Stem-loop binding involves a protein interface on the opposite side of the molecule from the active site where ssDNA is cleaved. Rep therefore has three distinct binding sites within its endonuclease domain for its different DNA substrates. Use of these different interfaces generates the structural asymmetry necessary to regulate later events in viral replication and integration.

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Related Citations: 

• Structural unity among viral origin binding proteins: crystal structure of the nuclease domain of adeno-associated virus Rep.
  Hickman, A.B., Ronning, D.R., Kotin, R.M., Dyda, F.
  (2002) Mol Cell 10: 327

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Organizational Affiliation: 

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Rep protein	C [auth A], D [auth B], E [auth C], F [auth D], G [auth E]	197	adeno-associated virus 5	Mutation(s): 0  Gene Names: rep, Rep22
UniProt
Find proteins for Q9YJC1 (adeno-associated virus 5) Explore Q9YJC1  Go to UniProtKB:  Q9YJC1

Entity ID: 1
Molecule	Chains	Length	Organism	Image
26-MER	A [auth F]	26	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
26-MER	B [auth G]	26	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.315 
• R-Value Work: 0.286 
• R-Value Observed: 0.286 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.671	α = 90
b = 131.706	β = 112.68
c = 82.164	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-17 
Deposition Author(s): Hickman, A.B., Ronning, D.R., Perez, Z.N., Kotin, R.M., Dyda, F.

Revision History  

• Version 1.0: 2004-02-17
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance