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- PDB-6gsi: Feline Calicivirus Strain F9 bound to a soluble ectodomain fragme... -

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Basic information

Entry
Database: PDB / ID: 6gsi
TitleFeline Calicivirus Strain F9 bound to a soluble ectodomain fragment of feline junctional adhesion molecule A - leading to assembly of a portal structure at a unique three-fold axis.
Components
  • Capsid proteinCapsid
  • Junctional adhesion molecule A
  • VP2
KeywordsVIRUS / Capsid / Calicivirus / Vesivirus / Vp1 / portal / Vp2 / junctional-adhesion molecule A
Function / homology
Function and homology information


regulation of membrane permeability / establishment of endothelial intestinal barrier / T=3 icosahedral viral capsid / intestinal absorption / bicellular tight junction / virion / host cell cytoplasm / cell adhesion / viral process / integral component of membrane / plasma membrane
Immunoglobulin-like fold / Immunoglobulin domain / Calicivirus coat protein / Protein of unknown function (DUF743) / Junctional adhesion molecule A / Immunoglobulin-like domain superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin V-set domain / Vesivirus VP2 ...Immunoglobulin-like fold / Immunoglobulin domain / Calicivirus coat protein / Protein of unknown function (DUF743) / Junctional adhesion molecule A / Immunoglobulin-like domain superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin V-set domain / Vesivirus VP2 / Immunoglobulin-like domain / Calicivirus coat protein / Immunoglobulin subtype / Immunoglobulin subtype 2 / Immunoglobulin V-set domain / Jelly Rolls - #20 / Jelly Rolls / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Junctional adhesion molecule A / Protein VP2 / Capsid protein
Biological speciesFelis catus (domestic cat)
Feline calicivirus strain F9
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 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 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Junctional adhesion molecule A
F: Junctional adhesion molecule A
G: Junctional adhesion molecule A
H: Junctional adhesion molecule A
I: VP2
J: VP2
K: VP2
L: VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)431,10516
Polymers430,94912
Non-polymers1564
Water0
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Junctional adhesion molecule A
F: Junctional adhesion molecule A
G: Junctional adhesion molecule A
H: Junctional adhesion molecule A
I: VP2
J: VP2
K: VP2
L: VP2
hetero molecules

A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Junctional adhesion molecule A
F: Junctional adhesion molecule A
G: Junctional adhesion molecule A
H: Junctional adhesion molecule A
I: VP2
J: VP2
K: VP2
L: VP2
hetero molecules

A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: Junctional adhesion molecule A
F: Junctional adhesion molecule A
G: Junctional adhesion molecule A
H: Junctional adhesion molecule A
I: VP2
J: VP2
K: VP2
L: VP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,293,31548
Polymers1,292,84636
Non-polymers46912
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation2
Buried area52450 Å2
ΔGint-260 kcal/mol
Surface area130440 Å2
MethodPISA

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Components

#1: Protein
Capsid protein / Capsid / Coat protein / CP / VP1


Mass: 73346.664 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Feline calicivirus strain F9 / References: UniProt: P27406
#2: Antibody
Junctional adhesion molecule A / JAM-A / Junctional adhesion molecule 1 / JAM-1


Mass: 22180.650 Da / Num. of mol.: 4 / Fragment: UNP residues 29-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Felis catus (domestic cat) / Gene: F11R, JAM1 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q2WGK2
#3: Protein
VP2 / Minor capsid protein


Mass: 12209.838 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Feline calicivirus strain F9 / References: UniProt: P28711
#4: Chemical
ChemComp-K / POTASSIUM ION / Potassium


Mass: 39.098 Da / Num. of mol.: 4 / 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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Feline calicivirus strain F9VIRUSVirus was propagated in Crandell Reese Feline Kidney cells1,2,30MULTIPLE SOURCES
2CapsidVIRUSIcosahedral Capsid11NATURAL
3feline junctional adhesion molecule ACOMPLEXSoluble ectodomain fragment comprising Ig-like domains D1 and D221RECOMBINANT
4VP2 - portal.COMPLEXPostulated to mediate endosome escape, this virion component is only present on the outer surface of the capsid following receptor engagement.31NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Feline calicivirus strain F911981
23Felis catus (domestic cat)9685
34Feline calicivirus strain F911981
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster) / Cell: CHO cells
Details of virus

Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION

IDEntity assembly-ID
11
22
Natural host

Ncbi tax-ID: 9685 / Organism: Felis catus

IDEntity assembly-ID
11
22
Virus shell

Diameter: 400 nm / Name: Capsid / Triangulation number (T number): 3

IDEntity assembly-ID
11
22
Buffer solutionpH: 7.2 / Details: Phosphate buffered saline
SpecimenConc.: 1 mg/ml
Details: Purified virions were incubated in the presence of purified ectodomain fragments.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/2
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
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
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: 13865
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: 129884 / Details: Autopicking in Relion
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58510
Details: Origins and orientations were originally assigned by 3D auto refinement with full icosahedral symmetry. Random group assignment was carried through the focussed classification process and used to divide the data into two roughly even halves that had been initially refined independently.
Symmetry type: POINT

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