2OBE

Crystal Structure of Chimpanzee Adenovirus (Type 68/Simian 25) Major Coat Protein Hexon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structure-based identification of a major neutralizing site in an adenovirus hexon

Pichla-Gollon, S.L.Drinker, M.Zhou, X.Xue, F.Rux, J.J.Gao, G.-P.Wilson, J.M.Ertl, H.C.J.Burnett, R.M.Bergelson, J.M.

(2007) J Virol 81: 1680-1689

  • DOI: https://doi.org/10.1128/JVI.02023-06
  • Primary Citation of Related Structures:  
    2OBE

  • PubMed Abstract: 

    Virus-specific neutralizing antibodies present an obstacle to the effective use of adenovirus vectors for gene therapy and vaccination. The specific sites recognized by neutralizing antibodies have not been identified for any adenovirus, but they have been proposed to reside within the hexon, in small regions of the molecule that are exposed on the capsid surface and possess sequences that vary among serotypes. We have mapped the epitopes recognized by a panel of seven hexon-specific monoclonal antibodies that neutralize the chimpanzee adenovirus 68 (AdC68). Surface plasmon resonance experiments revealed that the antibodies compete for a single hexon binding site, and experiments with synthetic peptides indicated that this site resides within just one small surface loop. Mutations within this loop (but not in other surface loops) permitted virus to escape neutralization by all seven monoclonal antibodies and to resist neutralization by polyclonal antisera obtained from animals immunized against AdC68. These results indicate that a single small surface loop defines a major neutralization site for AdC68 hexon.


  • Organizational Affiliation

    Abramson Research Center, Room 1205G, Immunologic and Infectious Disease, The Children's Hospital of Philadelphia, 3601 Civic Center Blvd., Pennsylvania, PA 19104, USA. [email protected]


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hexon protein
A, B, C
932Simian adenovirus 25Mutation(s): 0 
UniProt
Find proteins for Q8UY79 (Simian adenovirus 25)
Explore Q8UY79 
Go to UniProtKB:  Q8UY79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8UY79
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
FA [auth B]
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
LA [auth B],
M [auth A],
MA [auth B],
N [auth A],
O [auth A],
SA [auth C],
TA [auth C],
UA [auth C],
VA [auth C],
WA [auth C]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
2HP
Query on 2HP

Download Ideal Coordinates CCD File 
AA [auth B]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
AA [auth B],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
NA [auth C],
OA [auth C],
P [auth B],
PA [auth C],
Q [auth B],
QA [auth C],
R [auth B],
RA [auth C],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
DIHYDROGENPHOSPHATE ION
H2 O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.8α = 90
b = 433β = 90
c = 159.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 2.0: 2019-02-06
    Changes: Data collection, Database references, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-08-30
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary