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- PDB-3iy0: Variable domains of the x-ray structure of Fab 14 fitted into the... -

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Basic information

Entry
Database: PDB / ID: 3iy0
TitleVariable domains of the x-ray structure of Fab 14 fitted into the cryoEM reconstruction of the virus-Fab 14 complex
Components
  • Fab 14, heavy domainFragment antigen-binding
  • Fab 14, light domainFragment antigen-binding
KeywordsIMMUNE SYSTEM / cryoEM / neutralizing antibody / parvovirus / canine / feline / fab footprint
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsHafenstein, S. / Bowman, V.D. / Sun, T. / Nelson, C.D. / Palermo, L.M. / Chipman, P.R. / Battisti, A.J. / Parrish, C.R. / Rossmann, M.G.
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 Report
SummaryFull reportAbout validation report
History
DepositionApr 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Assembly

Deposited unit
L: Fab 14, light domain
H: Fab 14, heavy domain


Theoretical massNumber of molelcules
Total (without water)23,7922
Polymers23,7922
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody Fab 14, light domain / Fragment antigen-binding


Mass: 11737.015 Da / Num. of mol.: 1 / Fragment: Fab14 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab 14, heavy domain / Fragment antigen-binding


Mass: 12055.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeParent-ID
1FAB FRAGMENT OF MAB14 INTERACTING WITH CANINE PARVOVIRUSCOMPLEX0
2canine parvovirusVIRUS1
Details of virusHost category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Canis lupus familiaris
Virus shellTriangulation number (T number): 1
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Jun 17, 2004
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 45 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Calibrated magnification: 47190 X / Nominal defocus max: 3.8 nm / Nominal defocus min: 1 nm / Cs: 2 mm
Specimen holderTemperature: 93 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 37 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 109
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

CTF correctionDetails: ROBEM
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: COMMON LINES / Resolution: 12.5 Å / Num. of particles: 2059 / Symmetry type: POINT
RefinementHighest resolution: 12.5 Å
Refinement stepCycle: LAST / Highest resolution: 12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 0 0 1675

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