1M55 | pdb_00001m55

Catalytic domain of the Adeno Associated Virus type 5 Rep protein

• PDB DOI: https://doi.org/10.2210/pdb1M55/pdb

• Classification: VIRAL PROTEIN
• Organism(s): adeno-associated virus 5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-07-08 Released: 2002-08-28 
• Deposition Author(s): Hickman, A.B., Ronning, D.R., Kotin, R.M., Dyda, F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.196 (Depositor) 
• R-Value Work: 
  0.178 (Depositor) 

Literature

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: 327-337

• PubMed: 12191478 
• DOI: https://doi.org/10.1016/s1097-2765(02)00592-0
• Primary Citation Related Structures: 
  1M55


• PubMed Abstract: 
  

  Adeno-associated virus (AAV), unique among animal viruses in its ability to integrate into a specific chromosomal location, is a promising vector for human gene therapy. AAV Replication (Rep) protein is essential for viral replication and integration, and its amino terminal domain possesses site-specific DNA binding and endonuclease activities required for replication initiation and integration. This domain displays a novel endonuclease fold and demonstrates an unexpected structural relationship to other viral origin binding proteins such as the papillomavirus E1 protein and the SV40 T antigen. The active site, located at the bottom of a positively charged cleft, is formed by the spatial convergence of a divalent metal ion and two conserved sequence motifs that define the rolling circle replication superfamily.

---

Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA. [e-mail]

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: 46.02 kDa 
• Atom Count: 3,843 
• Modeled Residue Count: 386 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rep protein	A, B	197	adeno-associated virus 5	Mutation(s): 0
UniProt
Find proteins for Q9YJC1 (adeno-associated virus 5) Explore Q9YJC1  Go to UniProtKB:  Q9YJC1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A], F [auth B], G [auth B], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.196 (Depositor) 
• R-Value Work:  0.178 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.888	α = 90
b = 73.455	β = 94.491
c = 65.56	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-28 
Deposition Author(s): Hickman, A.B., Ronning, D.R., Kotin, R.M., Dyda, F.

Revision History  

• Version 1.0: 2002-08-28
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations