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- EMDB-0056: Feline Calicivirus Strain F9 bound to a soluble ectodomain fragme... -

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Basic information

Entry
Database: EMDB / ID: EMD-0056
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.
Map data
SampleFeline calicivirus strain F9:
(virus) x 2 / feline junctional adhesion molecule A / VP2 - portal. / Capsid proteinCapsid / Junctional adhesion molecule A / VP2 / ligand
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 subtype / Immunoglobulin subtype 2 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin-like fold / Immunoglobulin V-set domain / Vesivirus VP2 / Immunoglobulin-like domain / Calicivirus coat protein / Immunoglobulin-like domain superfamily / Junctional adhesion molecule A
Capsid protein / Protein VP2 / Junctional adhesion molecule A
Biological speciesFeline calicivirus strain F9 / Felis catus (domestic cat) / FCV (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsConley MJ / Bhella D
Funding support United Kingdom, 2 items
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 ReportPDB-ID: 6gsi

SummaryFull reportAbout validation report
History
DepositionJun 14, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseJan 16, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6gsi
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6gsi
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0056.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 600 pix.
= 639. Å
1.07 Å/pix.
x 600 pix.
= 639. Å
1.07 Å/pix.
x 600 pix.
= 639. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.11780139 - 0.21274377
Average (Standard dev.)0.00095921505 (±0.013303866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin300300300
Dimensions600600600
Spacing600600600
CellA=B=C: 639.00006 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z639.000639.000639.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS600600600
D min/max/mean-0.1180.2130.001

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Supplemental data

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Sample components

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Entire Feline calicivirus strain F9

EntireName: Feline calicivirus strain F9
Details: Virus was propagated in Crandell Reese Feline Kidney cells
Number of components: 8

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Component #1: virus, Feline calicivirus strain F9

VirusName: Feline calicivirus strain F9 / Class: VIRION
Details: Virus was propagated in Crandell Reese Feline Kidney cells
Empty: No / Enveloped: No / Isolate: STRAIN
Source (natural)Host Species: Felis catus (domestic cat)
Shell #1Name of element: Capsid / Diameter: 400.0 Å / T number (triangulation number): 3

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Component #2: virus, Feline calicivirus strain F9

VirusName: Feline calicivirus strain F9 / Class: VIRION / Details: Icosahedral CapsidCapsid / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Feline calicivirus strain F9
Source (natural)Host Species: Felis catus (domestic cat)
Shell #2Name of element: Capsid / Diameter: 400.0 Å / T number (triangulation number): 3

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Component #3: protein, feline junctional adhesion molecule A

ProteinName: feline junctional adhesion molecule A
Details: Soluble ectodomain fragment comprising Ig-like domains D1 and D2
Recombinant expression: No
SourceSpecies: Felis catus (domestic cat)
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster) / Cell of expression system: CHO cells

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Component #4: protein, VP2 - portal.

ProteinName: VP2 - portal.
Details: Postulated to mediate endosome escape, this virion component is only present on the outer surface of the capsid following receptor engagement.
Recombinant expression: No
SourceSpecies: Feline calicivirus strain F9

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Component #5: protein, Capsid protein

ProteinName: Capsid proteinCapsid / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 73.346664 kDa
SourceSpecies: FCV (virus)

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Component #6: protein, Junctional adhesion molecule A

ProteinName: Junctional adhesion molecule A / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 22.18065 kDa
SourceSpecies: Felis catus (domestic cat)
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

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Component #7: protein, VP2

ProteinName: VP2 / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 12.209838 kDa
SourceSpecies: FCV (virus)

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Component #8: ligand, POTASSIUM ION

LigandName: POTASSIUM IONPotassium / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 3.909805 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/mL / Buffer solution: Phosphate buffered saline / pH: 7.2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 63 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital 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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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 58510
Details: Images were motion-corrected using motioncor2 Defocus estimation was performed using GCTF
3D reconstructionSoftware: RELION
CTF correction: CTF correction was implemented through Relion
Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF
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.
FSC plot (resolution estimation)

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