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- PDB-3iy4: Variable domains of the computer generated model (WAM) of Fab 15 ... -

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Basic information

Entry
Database: PDB / ID: 3iy4
TitleVariable domains of the computer generated model (WAM) of Fab 15 fitted into the cryoEM reconstruction of the virus-Fab 15 complex
Components
  • fragment of neutralizing antibody 15 (heavy chain)
  • fragment of neutralizing antibody 15 (light chain)
KeywordsIMMUNE SYSTEM / cryoEM / neutralizing antibody / parvovirus / canine / feline / fab footprint
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.7 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 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

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Structure visualization

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Assembly

Deposited unit
A: fragment of neutralizing antibody 15 (light chain)
B: fragment of neutralizing antibody 15 (heavy chain)


Theoretical massNumber of molelcules
Total (without water)24,3382
Polymers24,3382
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody fragment of neutralizing antibody 15 (light chain)


Mass: 11970.164 Da / Num. of mol.: 1 / Fragment: fragment of neutralizing antibody 15 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody fragment of neutralizing antibody 15 (heavy chain)


Mass: 12367.916 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-IDSynonym
1Fab fragment from MAb 15 interacting with feline panleukopenia virus (FPV)Fragment antigen-bindingCOMPLEX0
2feline panleukopenia virusVIRUS1FPV
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Felis catus
Virus shellTriangulation number (T number): 1
Buffer solutionpH: 7.5 / Details: 10mM Tris-HCL
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10mM Tris-HCL
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 120 K / Method: blot before plunging

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Mar 29, 2004
Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Calibrated magnification: 47190 X / Nominal defocus max: 3.4 nm / Nominal defocus min: 0.9 nm
Astigmatism: astigmatism was corrected at 100,000 times magnification
Camera length: 0 mm
Specimen holderModel: GATAN LIQUID NITROGEN / Specimen holder type: side mounted nitrogen cooled / Temperature: 93 K / Temperature (max): 83 K / Temperature (min): 83 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 34.52 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansSampling size: 7 µm / Num. digital images: 50 / Od range: 0.9 / Scanner model: ZEISS SCAI
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EM3DR3D reconstruction
2EMPFT3D reconstruction
CTF correctionDetails: robem
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: common lines / Resolution: 11.7 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 4798 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 0 0 1713

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