[English] 日本語
- PDB-3iy1: Variable domains of the WAM of Fab B fitted into the cryoEM recon... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 3iy1
TitleVariable domains of the WAM of Fab B fitted into the cryoEM reconstruction of the virus-Fab B complex
  • Fab B, heavy chain
  • Fab B, light chain
KeywordsIMMUNE SYSTEM / cryoEM / neutralizing antibody / parvovirus / canine / feline / fab footprint
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 18 Å
AuthorsHafenstein, S. / Bowman, V.D. / Sun, T. / Nelson, C.D. / Palermo, L.M. / 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
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

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5106
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5106
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


Deposited unit
A: Fab B, light chain
B: Fab B, heavy chain

Theoretical massNumber of molelcules
Total (without water)23,4172

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


#1: Antibody Fab B, light chain

Mass: 11643.067 Da / Num. of mol.: 1 / Fragment: antibody B fragment / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
#2: Antibody Fab B, heavy chain

Mass: 11773.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)

Experimental details


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

Sample preparation

1Fab fragment from MAb B 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
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10mM Tris
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 120 K / Method: blot before plunging

Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Jun 30, 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: 3.7 nm / Nominal defocus min: 1.7 nm / 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: 28.4 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansSampling size: 7 µm / Details: scanned at 7 microns and bin averaged to 14 / Num. digital images: 56 / Od range: 0.9 / Scanner model: ZEISS SCAI
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1


EM software
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: 1126 / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 0 0 1648

About Yorodumi


Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • New page: Covid-19 featured information page in EM Navigator

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. New: Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more