1P2Z

Refinement of Adenovirus Type 2 Hexon with CNS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural and phylogenetic analysis of adenovirus hexons by use of high-resolution x-ray crystallographic, molecular modeling, and sequence-based methods

Rux, J.J.Kuser, P.R.Burnett, R.M.

(2003) J.VIROL. 77: 9553-9566

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A major impediment to the use of adenovirus as a gene therapy vector and for vaccine applications is the host immune response to adenovirus hexon-the major protein component of the icosahedral capsid. A solution may lie in novel vectors with modified ...

    A major impediment to the use of adenovirus as a gene therapy vector and for vaccine applications is the host immune response to adenovirus hexon-the major protein component of the icosahedral capsid. A solution may lie in novel vectors with modified or chimeric hexons designed to evade the immune response. To facilitate this approach, we have distinguished the portion of hexon that all serotypes have in common from the hypervariable regions that are responsible for capsid diversity and type-specific immunogenicity. The common hexon core-conserved because it forms the viral capsid-sets boundaries to the regions where modifications can be made to produce nonnative hexons. The core has been defined from the large and diverse set of known hexon sequences by an accurate alignment based on the newly refined crystal structures of human adenovirus types 2 (Ad2) and Ad5 hexon. Comparison of the two hexon models, which are the most accurate so far, reveals that over 90% of the residues in each have three-dimensional positions that closely match. Structures for more distant hexons were predicted by building molecular models of human Ad4, chimpanzee adenovirus (AdC68), and fowl adenovirus 1 (FAV1 or CELO). The five structures were then used to guide the alignment of the 40 full-length (>900 residues) hexon sequences in public databases. Distance- and parsimony-based phylogenetic trees are consistent and reveal evolutionary relationships between adenovirus types that parallel those of their animal hosts. The combination of crystallography, molecular modeling, and phylogenetic analysis defines a conserved molecular core that can serve as the armature for the directed design of novel hexons.


    Related Citations: 
    • Large-scale purification and crystallization of adenovirus hexon
      Rux, J.J.,Pascolini, D.,Burnett, R.M.
      (1999) ADENOVIRUS METHODS AND PROTOCOLS (IN: METHODS IN MOLECULAR MEDICINE, V.21) 21: 259
    • Type-specific epitope locations revealed by X-ray crystallographic study of adenovirus type 5 hexon.
      Rux, J.J.,Burnett, R.M.
      (2000) MOL.THER. 1: 18
    • The refined crystal structure of hexon, the major coat protein of adenovirus type 2, at 2.9 A resolution.
      Athappilly, F.K.,Murali, R.,Rux, J.J.,Cai, Z.,Burnett, R.M.
      (1994) J.Mol.Biol. 242: 430


    Organizational Affiliation

    The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hexon protein
A
967Human adenovirus C serotype 2Gene Names: L3
Find proteins for P03277 (Human adenovirus C serotype 2)
Go to UniProtKB:  P03277
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 150.540α = 90.00
b = 150.540β = 90.00
c = 150.540γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description