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TitleStructural comparison of different antibodies interacting with parvovirus capsids.
Journal, issue, pagesJ Virol, Vol. 83, Issue 11, Page 5556-5566, Year 2009
Publish dateMar 25, 2009
AuthorsSusan Hafenstein / Valorie D Bowman / Tao Sun / Christian D S Nelson / Laura M Palermo / Paul R Chipman / Anthony J Battisti / Colin R Parrish / Michael G Rossmann /
PubMed AbstractThe structures of canine parvovirus (CPV) and feline parvovirus (FPV) complexed with antibody fragments from eight different neutralizing monoclonal antibodies were determined by cryo-electron ...The structures of canine parvovirus (CPV) and feline parvovirus (FPV) complexed with antibody fragments from eight different neutralizing monoclonal antibodies were determined by cryo-electron microscopy (cryoEM) reconstruction to resolutions varying from 8.5 to 18 A. The crystal structure of one of the Fab molecules and the sequence of the variable domain for each of the Fab molecules have been determined. The structures of Fab fragments not determined crystallographically were predicted by homology modeling according to the amino acid sequence. Fitting of the Fab and virus structures into the cryoEM densities identified the footprints of each antibody on the viral surface. As anticipated from earlier analyses, the Fab binding sites are directed to two epitopes, A and B. The A site is on an exposed part of the surface near an icosahedral threefold axis, whereas the B site is about equidistant from the surrounding five-, three-, and twofold axes. One antibody directed to the A site binds CPV but not FPV. Two of the antibodies directed to the B site neutralize the virus as Fab fragments. The differences in antibody properties have been linked to the amino acids within the antibody footprints, the position of the binding site relative to the icosahedral symmetry elements, and the orientation of the Fab structure relative to the surface of the virus. Most of the exposed surface area was antigenic, although each of the antibodies had a common area of overlap that coincided with the positions of the previously mapped escape mutations.
External linksJ Virol / PubMed:19321620 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2 - 18 Å
Structure data

EMDB-5105: Canine parvovirus in complex with FAb from neutralizing antibody MAb 14
PDB-3iy0: Variable domains of the x-ray structure of Fab 14 fitted into the cryoEM reconstruction of the virus-Fab 14 complex
Method: EM (single particle) / Resolution: 12.5 Å

EMDB-5106: Fab from MAb B interacting with feline panleukopenia virus
PDB-3iy1: Variable domains of the WAM of Fab B fitted into the cryoEM reconstruction of the virus-Fab B complex
Method: EM (single particle) / Resolution: 18 Å

EMDB-5107: Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb 6
PDB-3iy2: Variable domains of the computer generated model (WAM) of Fab 6 fitted into the cryoEM reconstruction of the virus-Fab 6 complex
Method: EM (single particle) / Resolution: 18 Å

EMDB-5108: Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb 8
PDB-3iy3: Variable domains of the computer generated model (WAM) of Fab 8 fitted into the cryoEM reconstruction of the virus-Fab 8 complex
Method: EM (single particle) / Resolution: 11.1 Å

EMDB-5109: Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb 15
PDB-3iy4: Variable domains of the computer generated model (WAM) of Fab 15 fitted into the cryoEM reconstruction of the virus-Fab 15 complex
Method: EM (single particle) / Resolution: 11.7 Å

EMDB-5110: Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb 16
PDB-3iy5: Variable domains of the mouse Fab (1AIF) fitted into the cryoEM reconstruction of the virus-Fab 16 complex
Method: EM (single particle) / Resolution: 18 Å

EMDB-5111: Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb E
PDB-3iy6: Variable domains of the computer generated model (WAM) of Fab E fitted into the cryoEM reconstruction of the virus-Fab E complex
Method: EM (single particle) / Resolution: 12 Å

EMDB-5112: Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb F
PDB-3iy7: Variable domains of the computer generated model (WAM) of Fab F fitted into the cryoEM reconstruction of the virus-Fab F complex
Method: EM (single particle) / Resolution: 14 Å

PDB-3gk8:
X-ray crystal structure of the Fab from MAb 14, mouse antibody against Canine Parvovirus
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

Chemicals

ChemComp-HOH:
WATER / Water

Source
  • Canine parvovirus
  • Feline panleukopenia virus
  • mus musculus (house mouse)
  • rattus norvegicus (Norway rat)
Keywordsvirus / antigenic epitope / antibody / Fab / neutralizing / Amino Acid Sequence / Antibodies, Monoclonal / Antibody Specificity / Antigens / Capsid / Computational Biology / Conserved Sequence / Cryoelectron Microscopy / Crystallography, X-Ray / Immunoglobulin Fab Fragments / Models, Molecular / Molecular Sequence Data / Parvovirus / Protein Binding / Protein Structure, Quaternary / Protein Structure, Tertiary / Sequence Alignment / Structural Homology, Protein / IMMUNE SYSTEM / antibody fragment from neutralizing monoclonal antibody against canine parvovirus / cryoEM / neutralizing antibody / canine / feline / fab footprint

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