1S9H

Crystal Structure of Adeno-associated virus Type 2 Rep40

• PDB DOI: https://doi.org/10.2210/pdb1S9H/pdb

• Classification: REPLICATION
• Organism(s): adeno-associated virus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-02-04 Released: 2004-05-25 
• Deposition Author(s): James, J.A., Escalante, C.R., Yoon-Robarts, M., Edwards, T.A., Linden, R.M., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.293 (Depositor) 
• R-Value Work: 
  0.227 (Depositor) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal Structure of the SF3 Helicase from Adeno-Associated Virus Type 2

James, J.A., Escalante, C.R., Yoon-Robarts, M., Edwards, T.A., Linden, R.M., Aggarwal, A.K.

(2003) Structure 11: 1025-1035

• PubMed: 12906833 
• DOI: https://doi.org/10.1016/s0969-2126(03)00152-7
• Primary Citation of Related Structures:  
  1S9H


• PubMed Abstract: 
  

  We report here the crystal structure of an SF3 DNA helicase, Rep40, from adeno-associated virus 2 (AAV2). We show that AAV2 Rep40 is structurally more similar to the AAA(+) class of cellular proteins than to DNA helicases from other superfamilies. The structure delineates the expected Walker A and B motifs, but also reveals an unexpected "arginine finger" that directly implies the requirement of Rep40 oligomerization for ATP hydrolysis and helicase activity. Further, the Rep40 AAA(+) domain is novel in that it is unimodular as opposed to bimodular. Altogether, the structural connection to AAA(+) proteins defines the general architecture of SF3 DNA helicases, a family that includes simian virus 40 (SV40) T antigen, as well as provides a conceptual framework for understanding the role of Rep proteins during AAV DNA replication, packaging, and site-specific integration.

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Organizational Affiliation: 

Carl C. Icahn Center for Gene Therapy and Molecular Medicine, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, 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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 90.59 kDa 
• Atom Count: 5,963 
• Modelled Residue Count: 734 
• Deposited Residue Count: 804 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rep 40 protein	A, B, C	268	adeno-associated virus 2	Mutation(s): 0  Gene Names: REP EC: 3.6.4.12
UniProt
Find proteins for P03132 (Adeno-associated virus 2 (isolate Srivastava/1982)) Explore P03132  Go to UniProtKB:  P03132

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.293 (Depositor) 
• R-Value Work:  0.227 (Depositor) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.294	α = 90
b = 126.294	β = 90
c = 97.894	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-25 
Deposition Author(s): James, J.A., Escalante, C.R., Yoon-Robarts, M., Edwards, T.A., Linden, R.M., Aggarwal, A.K.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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