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- EMDB-5108: Feline panleukopenia virus in complex with FAb from neutralizing ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5108
TitleFeline panleukopenia virus in complex with FAb from neutralizing antibody MAb 8
Map dataFeline panleukopenia virus in complex with FAb from neutralizing antibody MAb 8
Sample
  • Sample: Fab fragment from MAb 8 interacting with feline panleukopenia virus (FPV)
  • Virus: Feline panleukopenia virus
Keywordsparvovirus / antigenic epitope / antibody / Fab / neutralizing
Biological speciesFeline panleukopenia virus
Methodsingle particle reconstruction / cryo EM / Resolution: 11.1 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.
History
DepositionMar 10, 2009-
Header (metadata) releaseApr 3, 2009-
Map releaseSep 30, 2009-
UpdateApr 16, 2014-
Current statusApr 16, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • 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-3iy3
  • Surface level: 1
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iy3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
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Supplemental images

emd_5108_1.png

Downloads & links

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Map

FileDownload / File: emd_5108.map.gz / Format: CCP4 / Size: 23.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFeline panleukopenia virus in complex with FAb from neutralizing antibody MAb 8
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.92 Å/pix.
x 184 pix.
= 537.28 Å		2.92 Å/pix.
x 184 pix.
= 537.28 Å		2.92 Å/pix.
x 184 pix.
= 537.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-3.04803133 - 6.91667986
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: 537.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.922.922.92
M x/y/z184184184
origin x/y/z0.0000.0000.000
length x/y/z537.280537.280537.280
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-3.0486.9170.000

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Supplemental data

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Sample components

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Entire : Fab fragment from MAb 8 interacting with feline panleukopenia vir...

EntireName: Fab fragment from MAb 8 interacting with feline panleukopenia virus (FPV)
Components
  • Sample: Fab fragment from MAb 8 interacting with feline panleukopenia virus (FPV)
  • Virus: Feline panleukopenia virus

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Supramolecule #1000: Fab fragment from MAb 8 interacting with feline panleukopenia vir...

SupramoleculeName: Fab fragment from MAb 8 interacting with feline panleukopenia virus (FPV)
type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Feline panleukopenia virus

SupramoleculeName: 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: Felis catus (domestic cat) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Diameter: 280 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.5 / Details: 10 mM Tris
GridDetails: quantifoils
VitrificationCryogen name: ETHANE / Chamber temperature: 120 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: plunger / Method: blot before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
TemperatureMin: 83 K / Max: 83 K / Average: 93 K
Alignment procedureLegacy - Astigmatism: lens astigmatism was corrected at 100,000 times magnification
DateJan 23, 2004
Image recordingCategory: 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 beamAcceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated 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 stageSpecimen holder: side mounted nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: robem
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMPFT EM3DR / Number images used: 4344

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