|Entry||Database: PDB / ID: 3iy2|
|Title||Variable domains of the computer generated model (WAM) of Fab 6 fitted into the cryoEM reconstruction of the virus-Fab 6 complex|
|Keywords||IMMUNE SYSTEM / cryoEM / neutralizing antibody / parvovirus / canine / feline / fab footprint|
|Biological species||Mus musculus (house mouse)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 18 Å|
|Authors||Hafenstein, S. / Bowman, V.D. / Sun, T. / Nelson, C.D. / Palermo, L.M. / Chipman, P.R. / Battisti, A.J. / Parrish, C.R. / Rossmann, M.G.|
|Citation||Journal: J Virol / Year: 2009|
Title: Structural comparison of different antibodies interacting with parvovirus capsids.
Authors: Susan 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 /
Abstract: 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 ...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.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
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A: Antibody 6, light chain
B: Antibody 6, heavy chain
|#1: Antibody|| |
Mass: 11739.198 Da / Num. of mol.: 1 / Fragment: fragment of antibody 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
|#2: Antibody|| |
Mass: 12260.739 Da / Num. of mol.: 1 / Fragment: FRAGMENT OF ANTIBODY 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Details of virus||Empty: YES / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION|
|Natural host||Organism: Felis catus|
|Virus shell||Triangulation number (T number): 1|
|Buffer solution||pH: 7.5 / Details: 10mM Tris-HCL|
|Specimen||Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10mM Tris-HCL|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 120 K / Method: blot before plunging|
-Electron microscopy imaging
|Microscopy||Model: FEI/PHILIPS CM300FEG/T / Date: Apr 15, 2005|
|Electron gun||Electron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Calibrated magnification: 47190 X / Nominal defocus max: 4.2 nm / Nominal defocus min: 1.2 nm|
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Camera length: 0 mm
|Specimen holder||Model: GATAN LIQUID NITROGEN / Specimen holder type: side mounted nitrogen cooled / Temperature: 93 K / Temperature (max): 93 K / Temperature (min): 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °|
|Image recording||Electron dose: 37 e/Å2 / Film or detector model: KODAK SO-163 FILM|
|Image scans||Sampling size: 7 µm / Details: scanned at 7 microns and bin averaged to 14 / Num. digital images: 42 / Od range: 0.9 / Scanner model: ZEISS SCAI|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M|
|Radiation wavelength||Relative weight: 1|
|CTF correction||Details: robem|
|Symmetry||Point symmetry: I (icosahedral)|
|3D reconstruction||Method: common lines / Resolution: 18 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 2520 / Symmetry type: POINT|
|Refinement step||Cycle: LAST|
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