|Entry||Database: EMDB / ID: EMD-5105|
|Title||Canine parvovirus in complex with FAb from neutralizing antibody MAb 14|
|Sample||Fab fragment of Mab14 interacting with canine parvovirus:|
|Keywords||virus / antigenic epitope / antibody / Fab / neutralizing|
|Biological species||Canine parvovirus (cpv)|
|Method||single particle reconstruction / cryo EM / Resolution: 12.5 Å|
|Authors||Hafenstein S / Bowman VD / Sun T / Nelson CDS / Palermo LM / Chipman PR / Battisti AJ / Parrish CR / Rossmann MG|
|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.
|Validation Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
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|File||Download / File: emd_5105.map.gz / Format: CCP4 / Size: 23.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.96 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Fab fragment of Mab14 interacting with canine parvovirus
|Entire||Name: Fab fragment of Mab14 interacting with canine parvovirus|
Number of components: 1
-Component #1: virus, Canine parvovirus
|Virus||Name: Canine parvovirus / a.k.a: cpv / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN|
|Species||Species: Canine parvovirus (cpv)|
|Source (natural)||Host Species: Canis lupus familiaris (dog) / Host category: VERTEBRATES|
|Shell #1||Name of element: cpv / Diameter: 280 Å / T number (triangulation number): 1|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 1 mg/mL / Buffer solution: 10mM Tris / pH: 7.5|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 120 K / Method: blot before plunging / Details: Vitrification instrument: plunger|
-Electron microscopy imaging
|Imaging||Microscope: FEI/PHILIPS CM300FEG/T / Date: Jun 17, 2004|
|Electron gun||Electron source: TUNGSTEN HAIRPIN / Accelerating voltage: 45 kV / Electron dose: 37 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Magnification: 45000 X (nominal), 47190 X (calibrated)|
Astigmatism: lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3800 nm
|Specimen Holder||Holder: side mounted nitrogen cooled / Model: GATAN LIQUID NITROGEN / Temperature: 93 (83 - 83 K)|
|Camera||Detector: KODAK SO-163 FILM|
|Image acquisition||Number of digital images: 109 / Scanner: ZEISS SCAI / Sampling size: 7 µm / Bit depth: 8 / OD range: 0.9 / Details: scanned at 7 microns and bin averaged to 14|
|Processing||Method: single particle reconstruction / Number of projections: 2059 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: common lines / Software: EMPFT EM3DR / CTF correction: robem / Resolution: 12.5 Å / Resolution method: FSC 0.5|
-Atomic model buiding
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