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- EMDB-2823: Structure determination of feline calicivirus virus-like particle... -

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Basic information

Entry
Database: EMDB / ID: EMD-2823
TitleStructure determination of feline calicivirus virus-like particles in the context of a pseudo-octahedral arrangement
Map dataReconstruction of feline calicivirus VLP T=1.
Sample
  • Sample: feline calicivirus virus-like particles
  • Virus: Canine calicivirus
Keywordsvirus-like particle / VLP / VP1 / calicivirus / FCV / icosahedral symmetry / octahedral symmetry / non-crystallographic symmetry / feline calici virus / vaccine / subviral particle
Function / homologyCalicivirus coat protein / Calicivirus coat protein / T=3 icosahedral viral capsid / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / Capsid protein VP1
Function and homology information
Biological speciesCanine calicivirus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 14.0 Å
AuthorsBurmeister WP / Buisson M / Estrozi LF / Schoehn G / Billet O / Hannas Z / Sigoillot-Claude C / Poulet H
CitationJournal: PLoS One / Year: 2015
Title: Structure determination of feline calicivirus virus-like particles in the context of a pseudo-octahedral arrangement.
Authors: Wim P Burmeister / Marlyse Buisson / Leandro F Estrozi / Guy Schoehn / Olivier Billet / Zahia Hannas / Cécile Sigoillot / Hervé Poulet /
Abstract: The vesivirus feline calicivirus (FCV) is a positive strand RNA virus encapsidated by an icosahedral T=3 shell formed by the viral VP1 protein. Upon its expression in the insect cell - baculovirus ...The vesivirus feline calicivirus (FCV) is a positive strand RNA virus encapsidated by an icosahedral T=3 shell formed by the viral VP1 protein. Upon its expression in the insect cell - baculovirus system in the context of vaccine development, two types of virus-like particles (VLPs) were formed, a majority built of 60 subunits (T=1) and a minority probably built of 180 subunits (T=3). The structure of the small particles was determined by x-ray crystallography at 0.8 nm resolution helped by cryo-electron microscopy in order to understand their formation. Cubic crystals belonged to space group P213. Their self-rotation function showed the presence of an octahedral pseudo-symmetry similar to the one described previously by Agerbandje and co-workers for human parvovirus VLPs. The crystal structure could be solved starting from the published VP1 structure in the context of the T=3 viral capsid. In contrast to viral capsids, where the capsomers are interlocked by the exchange of the N-terminal arm (NTA) domain, this domain is disordered in the T=1 capsid of the VLPs. Furthermore it is prone to proteolytic cleavage. The relative orientation of P (protrusion) and S (shell) domains is alerted so as to fit VP1 to the smaller T=1 particle whereas the intermolecular contacts around 2-fold, 3-fold and 5-fold axes are conserved. By consequence the surface of the VLP is very similar compared to the viral capsid and suggests a similar antigenicity. The knowledge of the structure of the VLPs will help to improve their stability, in respect to a use for vaccination.
History
DepositionNov 18, 2014-
Header (metadata) releaseNov 26, 2014-
Map releaseApr 1, 2015-
UpdateApr 15, 2015-
Current statusApr 15, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_2823.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of feline calicivirus VLP T=1.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.33 Å/pix.
x 150 pix.
= 350. Å		2.33 Å/pix.
x 150 pix.
= 350. Å		2.33 Å/pix.
x 150 pix.
= 350. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.33333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-5.52515793 - 5.53812361
Average (Standard dev.)0.0 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-75-75-75
Dimensions150150150
Spacing150150150
CellA=B=C: 350.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.33333333333332.33333333333332.3333333333333
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z350.000350.000350.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-75-75-75
NC/NR/NS150150150
D min/max/mean-5.5255.538-0.000

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Supplemental data

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Sample components

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Entire : feline calicivirus virus-like particles

EntireName: feline calicivirus virus-like particles
Components
  • Sample: feline calicivirus virus-like particles
  • Virus: Canine calicivirus

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Supramolecule #1000: feline calicivirus virus-like particles

SupramoleculeName: feline calicivirus virus-like particles / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1
Molecular weightTheoretical: 3.552 MDa

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Supramolecule #1: Canine calicivirus

SupramoleculeName: Canine calicivirus / type: virus / ID: 1 / NCBI-ID: 74724 / Sci species name: Canine calicivirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Felis catus (domestic cat) / synonym: VERTEBRATES
Host systemOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 / Recombinant plasmid: Merial100869
Molecular weightTheoretical: 3.5 MDa
Virus shellShell ID: 1 / Diameter: 280 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7 / Details: 20 mM MES pH 6, 200 mM NaCl
StainingType: NEGATIVE / Details: no stain (cryo-EM)
GridDetails: Quantifoil R2/1 holey grid
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
DateSep 1, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 20 / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Top-entry polara / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsParticles semi-automatically picked by the boxer program (EMAN)
CTF correctionDetails: Phase-flipping
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: OTHER / Software - Name: RIco, Bsoft, ctffind3, FPM / Number images used: 11158

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