3KIE

Crystal structure of adeno-associated virus serotype 3B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of adeno-associated virus serotype 3B (AAV-3B): insights into receptor binding and immune evasion.

Lerch, T.F.Xie, Q.Chapman, M.S.

(2010) Virology 403: 26-36

  • DOI: 10.1016/j.virol.2010.03.027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Adeno-associated viruses (AAVs) are leading candidate vectors for human gene therapy. AAV serotypes have broad cellular tropism and use a variety of cellular receptors. AAV serotype 3 binds to heparan sulfate proteoglycan prior to cell entry and is s ...

    Adeno-associated viruses (AAVs) are leading candidate vectors for human gene therapy. AAV serotypes have broad cellular tropism and use a variety of cellular receptors. AAV serotype 3 binds to heparan sulfate proteoglycan prior to cell entry and is serologically distinct from other serotypes. The capsid features that distinguish AAV-3B from other serotypes are poorly understood. The structure of AAV-3B has been determined to 2.6A resolution from twinned crystals of an infectious virus. The most distinctive structural features are located in regions implicated in receptor and antibody binding, providing insights into the cell entry mechanisms and antigenic nature of AAVs. We show that AAV-3B has a lower affinity for heparin than AAV-2, which can be rationalized by the distinct features of the AAV-3B capsid. The structure of AAV-3B provides an additional foundation for the future engineering of improved gene therapy vectors with modified receptor binding or antigenic characteristics.


    Related Citations: 
    • Twinned crystals of adeno-associated virus serotype 3b prove suitable for structural studies
      Lerch, T.F.,Xie, Q.,Ongley, H.M.,Hare, J.,Chapman, M.S.
      (2009) Acta Crystallogr.,Sect.F 65: 177


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, School of Medicine, Oregon Health & Science University, Portland, OR 97239-3098, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein VP1
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
736Adeno-associated virus 3BMutation(s): 0 
Find proteins for O56139 (Adeno-associated virus 3B)
Go to UniProtKB:  O56139
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D5M
Query on D5M

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O6 P
KHWCHTKSEGGWEX-RRKCRQDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.231 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 257.767α = 90.00
b = 257.767β = 90.00
c = 607.037γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
GLRFphasing
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description