1P30

Refinement of Adenovirus Type 5 Hexon with CNS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

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

  • DOI: 10.1128/jvi.77.17.9553-9566.2003
  • Primary Citation of Related Structures:  
    1P2Z, 1P30

  • 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 or chimeric hexons designed to evade the immune response ...

    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: 
    • 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
    • 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

    Organizational Affiliation

    The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hexon proteinA951Human adenovirus 5Mutation(s): 0 
Gene Names: L3
UniProt
Find proteins for P04133 (Human adenovirus C serotype 5)
Explore P04133 
Go to UniProtKB:  P04133
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04133
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.7α = 90
b = 150.7β = 90
c = 150.7γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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