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- PDB-3iy5: Variable domains of the mouse Fab (1AIF) fitted into the cryoEM r... -

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Basic information

Entry
Database: PDB / ID: 3iy5
TitleVariable domains of the mouse Fab (1AIF) fitted into the cryoEM reconstruction of the virus-Fab 16 complex
Components
  • antibody fragment IGG2A (heavy chain)
  • antibody fragment IGG2A (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: 18 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: antibody fragment IGG2A (light chain)
B: antibody fragment IGG2A (heavy chain)


Theoretical massNumber of molelcules
Total (without water)25,3862
Polymers25,3862
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody antibody fragment IGG2A (light chain)


Mass: 11631.756 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody antibody fragment IGG2A (heavy chain)


Mass: 13754.432 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: Jun 3, 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: 4.8 nm / Nominal defocus min: 0.4 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: 37.7 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansSampling size: 7 µm / Num. digital images: 48 / 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: 18 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 2084 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 1AIF

1aif

Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 0 0 1785

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