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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: 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 dataC3 reconstruction of Feline Calicivirus decorated with a soluble ectodomain fragment of the cellular receptor feline junctional adhesion molecule A.
SampleFeline calicivirus strain F9:
(virus) x 2 / feline junctional adhesion molecule A / VP2 - portal. / Capsid proteinCapsid / Junctional adhesion molecule A / VP2 / ligand
Function / homologyImmunoglobulin-like domain / Calicivirus coat protein / Protein of unknown function (DUF743) / Calicivirus coat protein / Immunoglobulin-like domain superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin-like fold / Immunoglobulin V-set domain / Vesivirus VP2 ...Immunoglobulin-like domain / Calicivirus coat protein / Protein of unknown function (DUF743) / Calicivirus coat protein / Immunoglobulin-like domain superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin-like fold / Immunoglobulin V-set domain / Vesivirus VP2 / Immunoglobulin subtype / Ig-like domain profile. / Immunoglobulin subtype 2 / Immunoglobulin V-set domain / regulation of membrane permeability / establishment of endothelial intestinal barrier / T=3 icosahedral viral capsid / intestinal absorption / bicellular tight junction / virion / host cell cytoplasm / viral process / integral component of membrane / plasma membrane / Capsid protein / Protein VP2 / Junctional adhesion molecule A
Function and homology information
SourceFeline calicivirus strain F9 / Felis catus (domestic cat) / FCV (virus)
Methodsingle particle reconstruction / cryo EM / 3.75 Å resolution
AuthorsConley MJ / Bhella D
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
Validation ReportPDB-ID: 6gsi

SummaryFull reportAbout validation report
DateDeposition: Jun 14, 2018 / Header (metadata) release: Aug 22, 2018 / Map release: Jan 16, 2019 / Last update: Jan 30, 2019

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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

Fileemd_0056.map.gz (map file in CCP4 format, 864001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
1.07 Å/pix.
= 639. Å
600 pix
1.07 Å/pix.
= 639. Å
600 pix
1.07 Å/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 Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.11780139 - 0.21274377
Average (Standard dev.)0.00095921505 (0.013303866)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions600600600
Origin300.0300.0300.0
Limit899.0899.0899.0
Spacing600600600
CellA=B=C: 639.00006 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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
Raw dataEMPIAR-10193 (Title: Calicivirus VP2 forms a portal to mediate endosome escape
Data size: 867.0
Data #1: Motion corrected micrographs of feline calicivirus strain F9 decorated with feline junctional adhesion molecule A [micrographs - single frame])

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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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