5BYG

X-ray structure of AAV2 OBD-AAVS1 complex 2:1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural Insights into the Assembly of the Adeno-associated Virus Type 2 Rep68 Protein on the Integration Site AAVS1.

Musayev, F.N.Zarate-Perez, F.Bishop, C.Burgner, J.W.Escalante, C.R.

(2015) J.Biol.Chem. 290: 27487-27499

  • DOI: 10.1074/jbc.M115.669960
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Adeno-associated virus (AAV) is the only eukaryotic virus with the property of establishing latency by integrating site-specifically into the human genome. The integration site known as AAVS1 is located in chromosome 19 and contains multiple GCTC rep ...

    Adeno-associated virus (AAV) is the only eukaryotic virus with the property of establishing latency by integrating site-specifically into the human genome. The integration site known as AAVS1 is located in chromosome 19 and contains multiple GCTC repeats that are recognized by the AAV non-structural Rep proteins. These proteins are multifunctional, with an N-terminal origin-binding domain (OBD) and a helicase domain joined together by a short linker. As a first step to understand the process of site-specific integration, we proceeded to characterize the recognition and assembly of Rep68 onto the AAVS1 site. We first determined the x-ray structure of AAV-2 Rep68 OBD in complex with the AAVS1 DNA site. Specificity is achieved through the interaction of a glycine-rich loop that binds the major groove and an α-helix that interacts with a downstream minor groove on the same face of the DNA. Although the structure shows a complex with three OBD molecules bound to the AAVS1 site, we show by using analytical centrifugation and electron microscopy that the full-length Rep68 forms a heptameric complex. Moreover, we determined that a minimum of two direct repeats is required to form a stable complex and to melt DNA. Finally, we show that although the individual domains bind DNA poorly, complex assembly requires oligomerization and cooperation between its OBD, helicase, and the linker domains.


    Organizational Affiliation

    From the Department of Medicinal Chemistry, School of Pharmacy, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein Rep78
A, B, C, D
213Adeno-associated virus 2 (isolate Srivastava/1982)Mutation(s): 2 
Gene Names: Rep78
Find proteins for Q89268 (Adeno-associated virus 2 (isolate Srivastava/1982))
Go to UniProtKB:  Q89268
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*CP*GP*GP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*TP*CP*GP*CP*T)-3')E,G21Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*AP*GP*CP*GP*CP*CP*GP*A)-3')F,H21Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, C
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 183.136α = 90.00
b = 79.595β = 98.12
c = 139.502γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM09285

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references
  • Version 1.2: 2015-11-25
    Type: Database references
  • Version 1.3: 2017-08-09
    Type: Database references, Derived calculations
  • Version 1.4: 2017-09-13
    Type: Author supporting evidence