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- EMDB-5110: Feline panleukopenia virus in complex with FAb from neutralizing ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5110 | |||||||||
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Title | Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb 16 | |||||||||
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![]() | Fab fragment from MAb 15 interacting with feline panleukopenia virus (FPV)![]() virus ![]() | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Hafenstein S / Bowman VD / Sun T / Nelson CDS / Palermo LM / Chipman PR / Battisti AJ / Parrish CR / Rossmann MG | |||||||||
![]() | ![]() 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 | ![]() ![]() ![]() ![]() | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
Header (meta data in XML format) |
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Images |
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Archive directory |
-Related structure data
Related structure data | ![]() 3iy5CM ![]() 5105C ![]() 5106C ![]() 5107C ![]() 5108C ![]() 5109C ![]() 5111C ![]() 5112C ![]() 3gk8C ![]() 3iy0C ![]() 3iy1C ![]() 3iy2C ![]() 3iy3C ![]() 3iy4C ![]() 3iy6C ![]() 3iy7C C: citing same article ( M: atomic model generated by this map |
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Similar-shape strucutres |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.88 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire Fab fragment from MAb 15 interacting with feline panleukopenia vi...
Entire | Name: Fab fragment from MAb 15 interacting with feline panleukopenia virus (FPV)![]() Number of components: 2 |
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-Component #1: virus, Feline panleukopenia virus
Virus | Name: Feline panleukopenia virus / a.k.a: FPV / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN |
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Species | Species: ![]() ![]() |
Source (natural) | Host Species: ![]() ![]() ![]() |
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | Specimen conc.: 1 mg/mL / Buffer solution: 10mM Tris-HCL / pH: 7.5 |
Support film | quantifoils |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 120 K / Method: blot before plunging / Details: Vitrification instrument: plunger |
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Electron microscopy imaging
![]() | Microscope: FEI/PHILIPS CM300FEG/T / Date: Jun 3, 2004 |
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Electron gun | Electron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Electron dose: 37.7 e/Å2 / Illumination mode: FLOOD BEAM |
Lens | Magnification: 45000 X (nominal), 47190 X (calibrated) Astigmatism: astigmatism was corrected at 100,000 times magnification Cs: 2 mm / Imaging mode: BRIGHT FIELD ![]() |
Specimen Holder | Holder: side mounted nitrogen cooled / Model: GATAN LIQUID NITROGEN / Temperature: 93 (83 - 83 K) |
Camera | Detector: KODAK SO-163 FILM |
-Image acquisition
Image acquisition | Number of digital images: 48 / Scanner: ZEISS SCAI / Sampling size: 7 µm / Bit depth: 8 / OD range: 0.9 |
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Image processing
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3D reconstruction | Algorithm: common lines / Software: EMPFT EM3DR / CTF correction: robem / Resolution: 18 Å / Resolution method: FSC 0.5 |
-Atomic model buiding
Output model |
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