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Open data
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Basic information
Entry | Database: PDB / ID: 4pb6 | ||||||
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Title | Feline calicivirus VP1 T=1 virus-like particle | ||||||
![]() | VP1 | ||||||
![]() | VIRUS / viral capsid protein / virus-like particle | ||||||
Function / homology | T=3 icosahedral viral capsid / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Capsid protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Burmeister, W.P. / Buisson, M. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 737.8 KB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 518.9 KB | Display | |
Data in CIF | ![]() | 669.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2823C ![]() 3m8lS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 |
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3 | ![]()
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: C3 (3 fold cyclic)) | ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 59297.613 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62 % / Description: tetrahedra or octahedra |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: reservoir solution: 7 - 10 % PEG 6000, 0.1 M Hepes pH 7, 0.5 - 1 M LiCl protein in: 20 mM MES pH 6, 200 mM NaCl at 3.4 mg/ml |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9185 Å / Relative weight: 1 |
Reflection | Resolution: 8→67.2 Å / Num. all: 14809 / Num. obs: 14809 / % possible obs: 87.22 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.24 / Rsym value: 0.24 / Net I/av σ(I): 6.64 / Net I/σ(I): 3.07 |
Reflection shell | Resolution: 8→8.43 Å / Redundancy: 1.82 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 0.69 / % possible all: 61.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb 3m8l and model builting Resolution: 8→65.51 Å / Cor.coef. Fo:Fc: 0.503 / Cor.coef. Fo:Fc free: 0.42 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 8.911 / ESU R Free: 9.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||
Displacement parameters | Biso mean: 94.995 Å2
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Refinement step | Cycle: 1 / Resolution: 8→65.51 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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