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- EMDB-0054: Feline Calicivirus Strain F9 -

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Basic information

Entry
Database: EMDB / ID: 0054
TitleFeline Calicivirus Strain F9
Map dataIcosahedral reconstruction of feline calicivirus strain F9
SampleT=3 Icosahedral Capsid.:
VP1 / ligand
Function / homologyCalicivirus coat protein / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / Calicivirus coat protein / VP1
Function and homology information
SourceFeline calicivirus
Methodsingle particle reconstruction / cryo EM / 3 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: 6gsh

SummaryFull reportAbout validation report
DateDeposition: Jun 14, 2018 / Header (metadata) release: Aug 22, 2018 / Map release: Jan 16, 2019 / Last update: Feb 6, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0054.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.07 Å/pix.
= 545.28 Å
512 pix
1.07 Å/pix.
= 545.28 Å
512 pix
1.07 Å/pix.
= 545.28 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-0.25493634 - 0.45862737
Average (Standard dev.)0.0027425927 (0.027666343)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin0.00.00.0
Limit511.0511.0511.0
Spacing512512512
CellA=B=C: 545.28 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/z512512512
origin x/y/z0.0000.0000.000
length x/y/z545.280545.280545.280
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.2550.4590.003

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Supplemental data

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Sample components

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Entire T=3 Icosahedral Capsid.

EntireName: T=3 Icosahedral Capsid. / Details: T=3 Icosahedral Capsid / Number of components: 3

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Component #1: protein, T=3 Icosahedral Capsid.

ProteinName: T=3 Icosahedral Capsid. / Details: T=3 Icosahedral Capsid / Recombinant expression: No
SourceSpecies: Feline calicivirus
Source (engineered)Expression System: Felis catus (domestic cat)

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Component #2: protein, VP1

ProteinName: VP1 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 73.346664 kDa
SourceSpecies: Feline calicivirus
Source (engineered)Expression System: Felis catus (domestic cat)

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Component #3: ligand, POTASSIUM ION

LigandName: POTASSIUM IONPotassium / Number of Copies: 3 / 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: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5198
Details: Each micrograph was recorded as a movie of 50 individual fractions with a total dose of 63 e/angstrom squared
Raw dataEMPIAR-10192 (Title: Calicivirus VP2 forms a portal to mediate endosome escape
Data size: 324.9
Data #1: Motion corrected micrographs of feline calicivirus strain F9 [micrographs - single frame])

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 41436
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 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

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