T=3 icosahedral viral capsid / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Capsid protein
Function and homology information
Biological species
Canine calicivirus
Method
single particle reconstruction / cryo EM / negative staining / Resolution: 14.0 Å
Journal: 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
Deposition
Nov 18, 2014
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Header (metadata) release
Nov 26, 2014
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Map release
Apr 1, 2015
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Update
Apr 15, 2015
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Current status
Apr 15, 2015
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Shell ID: 1 / Diameter: 280 Å / T number (triangulation number): 1
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Experimental details
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Structure determination
Method
negative staining, cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Buffer
pH: 7 / Details: 20 mM MES pH 6, 200 mM NaCl
Staining
Type: NEGATIVE / Details: no stain (cryo-EM)
Grid
Details: Quantifoil R2/1 holey grid
Vitrification
Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI POLARA 300
Date
Sep 1, 2010
Image recording
Category: 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 beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Specimen holder: Top-entry polara / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
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Image processing
Details
Particles semi-automatically picked by the boxer program (EMAN)
CTF correction
Details: Phase-flipping
Final reconstruction
Applied 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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