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- PDB-6gsh: Feline Calicivirus Strain F9 -

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Basic information

Entry
Database: PDB / ID: 6gsh
TitleFeline Calicivirus Strain F9
ComponentsVP1
KeywordsVIRUS / Capsid / Calicivirus / Vesivirus / Vp1
Function / homologyCalicivirus coat protein / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Calicivirus coat protein / Jelly Rolls - #20 / Jelly Rolls / Sandwich / Mainly Beta / VP1
Function and homology information
Biological speciesFeline calicivirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsConley, M.J. / Bhella, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UU_12014/7 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J013854/1 United Kingdom
CitationJournal: Nature / Year: 2019
Title: Calicivirus VP2 forms a portal-like assembly following receptor engagement.
Authors: Michaela J Conley / Marion McElwee / Liyana Azmi / Mads Gabrielsen / Olwyn Byron / Ian G Goodfellow / David Bhella /
Abstract: To initiate infection, many viruses enter their host cells by triggering endocytosis following receptor engagement. However, the mechanisms by which non-enveloped viruses escape the endosome are ...To initiate infection, many viruses enter their host cells by triggering endocytosis following receptor engagement. However, the mechanisms by which non-enveloped viruses escape the endosome are poorly understood. Here we present near-atomic-resolution cryo-electron microscopy structures for feline calicivirus both undecorated and labelled with a soluble fragment of its cellular receptor, feline junctional adhesion molecule A. We show that VP2, a minor capsid protein encoded by all caliciviruses, forms a large portal-like assembly at a unique three-fold axis of symmetry, following receptor engagement. This assembly-which was not detected in undecorated virions-is formed of twelve copies of VP2, arranged with their hydrophobic N termini pointing away from the virion surface. Local rearrangement at the portal site leads to the opening of a pore in the capsid shell. We hypothesize that the portal-like assembly functions as a channel for the delivery of the calicivirus genome, through the endosomal membrane, into the cytoplasm of a host cell, thereby initiating infection. VP2 was previously known to be critical for the production of infectious virus; our findings provide insights into its structure and function that advance our understanding of the Caliciviridae.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 6, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.4Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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  • Biological unit as author_and_software_defined_assembly
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP1
C: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,1576
Polymers220,0403
Non-polymers1173
Water0
1
A: VP1
B: VP1
C: VP1
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)13,209,437360
Polymers13,202,400180
Non-polymers7,038180
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
MethodPISA

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Components

#1: Protein VP1


Mass: 73346.664 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline calicivirus / Cell (production host): Crandell Reese Feline Kidney cells
Cell line (production host): Crandell Reese Feline Kidney cells
Production host: Felis catus (domestic cat) / References: UniProt: A2T4P8
#2: Chemical ChemComp-K / POTASSIUM ION / Potassium


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: T=3 Icosahedral Capsid. / Type: COMPLEX / Details: T=3 Icosahedral Capsid / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Feline calicivirus
Source (recombinant)Organism: Felis catus (domestic cat)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Felis catus
Virus shellName: Capsid / Diameter: 400 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.2 / Details: Phosphate buffered saline
SpecimenConc.: 1 mg/ml / Details: Purified enveloped virions / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Cs: 2.7 mm
Image recordingElectron dose: 63 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5198
Details: Each micrograph was recorded as a movie of 50 individual fractions with a total dose of 63 e/angstrom squared

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
Image processingDetails: Images were motion-corrected using motioncor2 Defocus estimation was performed using GCTF
CTF correctionDetails: CTF correction was implemented through Relion / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 59531 / Details: Autopicking in Relion
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41436 / Symmetry type: POINT

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