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- EMDB-5105: Canine parvovirus in complex with FAb from neutralizing antibody ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5105
TitleCanine parvovirus in complex with FAb from neutralizing antibody MAb 14
Map data
SampleFab fragment of Mab14 interacting with canine parvovirus:
virus
Keywordsvirus / antigenic epitope / antibody / Fab / neutralizing
Biological speciesCanine parvovirus (cpv)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsHafenstein S / Bowman VD / Sun T / Nelson CDS / Palermo LM / Chipman PR / Battisti AJ / Parrish CR / Rossmann MG
CitationJournal: 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 ReportSummary, Full report, XML, About validation report
History
DepositionMar 9, 2009-
Header (metadata) releaseApr 3, 2009-
Map releaseApr 15, 2009-
UpdateApr 16, 2014-
Current statusApr 16, 2014Processing site: RCSB / Status: Released

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Structure visualization

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  • Surface view with section colored by density value
  • Surface level: 1
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  • Surface view colored by radius
  • Surface level: 1
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  • Surface view with fitted model
  • Atomic models: PDB-3iy0
  • Surface level: 1
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iy0
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5105.map.gz / Format: CCP4 / Size: 23.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.96 Å/pix.
x 184 pix.
= 544.64 Å
2.96 Å/pix.
x 184 pix.
= 544.64 Å
2.96 Å/pix.
x 184 pix.
= 544.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.96 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-2.58916688 - 6.42649269
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-92-92-92
Dimensions184184184
Spacing184184184
CellA=B=C: 544.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.962.962.96
M x/y/z184184184
origin x/y/z0.0000.0000.000
length x/y/z544.640544.640544.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-92-92-92
NC/NR/NS184184184
D min/max/mean-2.5896.4260.000

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Supplemental data

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Sample components

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Entire Fab fragment of Mab14 interacting with canine parvovirus

EntireName: Fab fragment of Mab14 interacting with canine parvovirus
Number of components: 1

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Component #1: virus, Canine parvovirus

VirusName: Canine parvovirus / a.k.a: cpv / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Canine parvovirus (cpv)
Source (natural)Host Species: Canis lupus familiaris (dog) / Host category: VERTEBRATES
Shell #1Name of element: cpv / Diameter: 280 Å / T number (triangulation number): 1

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / Buffer solution: 10mM Tris / pH: 7.5
Support filmquantifoils
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 120 K / Method: blot before plunging / Details: Vitrification instrument: plunger

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM300FEG/T / Date: Jun 17, 2004
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 45 kV / Electron dose: 37 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 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 HolderHolder: side mounted nitrogen cooled / Model: GATAN LIQUID NITROGEN / Temperature: 93 (83 - 83 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber 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

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 2059 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: common lines / Software: EMPFT EM3DR / CTF correction: robem / Resolution: 12.5 Å / Resolution method: FSC 0.5

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Atomic model buiding

Output model

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