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- EMDB-6629: Near-atomic structure of Canine Parvovirus complexed with Fab E -

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Basic information

Entry
Database: EMDB / ID: EMD-6629
TitleNear-atomic structure of Canine Parvovirus complexed with Fab E
Map dataReconstruction of CPV-FAB E complex
Sample
  • Sample: Canine Parvovirus complexed with Fab E
  • Virus: Canine parvovirus
  • Protein or peptide: Fab E
Keywordsparvovirus / single particle / canine parvovirus / fab / antibody / complex
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat) / Canine parvovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsOrgantini LJ / Hafenstein S
CitationJournal: J Virol / Year: 2016
Title: Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus.
Authors: Lindsey J Organtini / Hyunwook Lee / Sho Iketani / Kai Huang / Robert E Ashley / Alexander M Makhov / James F Conway / Colin R Parrish / Susan Hafenstein /
Abstract: Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was ...Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM.
IMPORTANCE: Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced ...IMPORTANCE: Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time.
History
DepositionMar 18, 2016-
Header (metadata) releaseMar 30, 2016-
Map releaseMar 30, 2016-
UpdateNov 2, 2016-
Current statusNov 2, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3jcx
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3jcx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6629.gif

Downloads & links

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Map

FileDownload / File: emd_6629.map.gz / Format: CCP4 / Size: 159.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of CPV-FAB E complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 350 pix.
= 479.5 Å		1.37 Å/pix.
x 350 pix.
= 479.5 Å		1.37 Å/pix.
x 350 pix.
= 479.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-14.583890909999999 - 16.665075300000002
Average (Standard dev.)0.00137222 (±0.99988419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 479.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z479.500479.500479.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-14.58416.6650.001

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Supplemental data

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Sample components

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Entire : Canine Parvovirus complexed with Fab E

EntireName: Canine Parvovirus complexed with Fab E
Components
  • Sample: Canine Parvovirus complexed with Fab E
  • Virus: Canine parvovirus
  • Protein or peptide: Fab E

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Supramolecule #1000: Canine Parvovirus complexed with Fab E

SupramoleculeName: Canine Parvovirus complexed with Fab E / type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Canine parvovirus

SupramoleculeName: Canine parvovirus / type: virus / ID: 1 / Name.synonym: CPV / NCBI-ID: 10788 / Sci species name: Canine parvovirus / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: CPV
Host (natural)Organism: Canis lupus (gray wolf) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: VP2 / Diameter: 260 Å / T number (triangulation number): 1

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Macromolecule #1: Fab E

MacromoleculeName: Fab E / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: B5A8 / synonym: rat

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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: 7.4 / Details: PBS
GridDetails: Quantifoil
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI POLARA 300
DateDec 20, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1424 / Average electron dose: 30 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTFFIND4
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 47563

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