[English] 日本語
![](img/lk-miru.gif)
- EMDB-5108: Feline panleukopenia virus in complex with FAb from neutralizing ... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-5108 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb 8 | |||||||||
![]() | Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb 8 | |||||||||
![]() |
| |||||||||
![]() | parvovirus / antigenic epitope / antibody / Fab / neutralizing | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.1 Å | |||||||||
![]() | 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. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 4.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 10.4 KB 10.4 KB | Display Display | ![]() |
Images | ![]() | 289.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3iy3MC ![]() 5105C ![]() 5106C ![]() 5107C ![]() 5109C ![]() 5110C ![]() 5111C ![]() 5112C ![]() 3gk8C ![]() 3iy0C ![]() 3iy1C ![]() 3iy2C ![]() 3iy4C ![]() 3iy5C ![]() 3iy6C ![]() 3iy7C M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Feline panleukopenia virus in complex with FAb from neutralizing antibody MAb 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.92 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Fab fragment from MAb 8 interacting with feline panleukopenia vir...
Entire | Name: Fab fragment from MAb 8 interacting with feline panleukopenia virus (FPV) |
---|---|
Components |
|
-Supramolecule #1000: Fab fragment from MAb 8 interacting with feline panleukopenia vir...
Supramolecule | Name: Fab fragment from MAb 8 interacting with feline panleukopenia virus (FPV) type: sample / ID: 1000 / Number unique components: 2 |
---|
-Supramolecule #1: Feline panleukopenia virus
Supramolecule | Name: Feline panleukopenia virus / type: virus / ID: 1 / Name.synonym: FPV / NCBI-ID: 10786 / Sci species name: Feline panleukopenia virus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: FPV |
---|---|
Host (natural) | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / Diameter: 280 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 1.0 mg/mL |
---|---|
Buffer | pH: 7.5 / Details: 10 mM Tris |
Grid | Details: quantifoils |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 120 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: blot before plunging |
-
Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/T |
---|---|
Temperature | Min: 83 K / Max: 83 K / Average: 93 K |
Alignment procedure | Legacy - Astigmatism: lens astigmatism was corrected at 100,000 times magnification |
Date | Jan 23, 2004 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 49 / Average electron dose: 25.44 e/Å2 / Details: scanned at 7 microns and bin averaged to 14 / Od range: 0.9 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Calibrated magnification: 47190 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder: side mounted nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN |
-
Image processing
CTF correction | Details: robem |
---|---|
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMPFT EM3DR / Number images used: 4344 |