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- PDB-4pb6: Feline calicivirus VP1 T=1 virus-like particle -

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Basic information

Entry
Database: PDB / ID: 4pb6
TitleFeline calicivirus VP1 T=1 virus-like particle
ComponentsVP1
KeywordsVIRUS / viral capsid protein / virus-like 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 speciesFeline calicivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 8 Å
AuthorsBurmeister, W.P. / Buisson, M.
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
DepositionApr 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy
Category: database_PDB_rev / database_PDB_rev_record / entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
K: VP1
L: VP1
M: VP1
N: VP1
O: VP1
P: VP1
Q: VP1
R: VP1
S: VP1
T: VP1


Theoretical massNumber of molelcules
Total (without water)1,185,95220
Polymers1,185,95220
Non-polymers00
Water00
1
A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
K: VP1
L: VP1
M: VP1
N: VP1
O: VP1
P: VP1
Q: VP1
R: VP1
S: VP1
T: VP1

A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
K: VP1
L: VP1
M: VP1
N: VP1
O: VP1
P: VP1
Q: VP1
R: VP1
S: VP1
T: VP1

A: VP1
B: VP1
C: VP1
D: VP1
E: VP1
F: VP1
G: VP1
H: VP1
I: VP1
J: VP1
K: VP1
L: VP1
M: VP1
N: VP1
O: VP1
P: VP1
Q: VP1
R: VP1
S: VP1
T: VP1


Theoretical massNumber of molelcules
Total (without water)3,557,85760
Polymers3,557,85760
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)358.336, 358.336, 358.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
SymmetryPoint symmetry: (Schoenflies symbol: C3 (3 fold cyclic))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(1), (1), (1)
3generate(1), (1), (1)

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Components

#1: Protein
VP1


Mass: 59297.613 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline calicivirus / Strain: Merial100869 / Gene: VP1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0J9X1Z3*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62 % / Description: tetrahedra or octahedra
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9185 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9185 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
Cootmodel building
REFMAC5.7.0029refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 3m8l and model builting

3m8l


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
RfactorNum. reflection% reflectionSelection details
Rfree0.46285 710 4.9 %RANDOM
Rwork0.44128 ---
obs0.44232 13781 87.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 94.995 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 8→65.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms77840 0 0 0 77840
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
8-8.4330.589846.20.56127460.87
8.94-9.560.41814.20.43182997.5

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