|Entry||Database: EMDB / ID: EMD-5106|
|Title||Fab from MAb B interacting with feline panleukopenia virusFragment antigen-binding|
|Sample||Fab fragment from MAb B interacting with feline panleukopenia virus (FPV)Fragment antigen-binding:|
|Keywords||parvovirus / antigenic epitope / antibody / Fab / neutralizing|
|Biological species||Feline panleukopenia virus (FPV)|
|Method||single particle reconstruction / cryo EM / Resolution: 18 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: |
Downloads & links
|File||Download / File: emd_5106.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: 2.89 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Fab fragment from MAb B interacting with feline panleukopenia vir...
|Entire||Name: Fab fragment from MAb B interacting with feline panleukopenia virus (FPV)Fragment antigen-binding|
Number of components: 2
-Component #1: virus, Feline panleukopenia virus
|Virus||Name: Feline panleukopenia virus / a.k.a: FPV / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: Feline panleukopenia virus (FPV)|
|Source (natural)||Host Species: Felis catus (domestic cat) / Host category: VERTEBRATES|
|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 30, 2004|
|Electron gun||Electron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Electron dose: 28.4 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 45000 X (nominal), 47190 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1700 - 3700 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: 56 / 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: 1126 / Applied symmetry: I (icosahedral)|
|3D reconstruction||Algorithm: common lines / Software: EMPFT EM3DR / CTF correction: robem / Resolution: 18 Å / Resolution method: FSC 0.5|
-Atomic model buiding
-Aug 12, 2020. New: Covid-19 info
New: Covid-19 info
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi