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- EMDB-0054: Feline Calicivirus Strain F9 -

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Basic information

Entry
Database: EMDB / ID: EMD-0054
TitleFeline Calicivirus Strain F9
Map data
SampleT=3 Icosahedral Capsid.:
VP1 / ligand
Function / homologyCalicivirus coat protein / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / VP1
Function and homology information
Biological speciesFeline calicivirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3 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: 6gsh

SummaryFull reportAbout validation report
History
DepositionJun 14, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseJan 16, 2019-
UpdateDec 11, 2019-
Current statusDec 11, 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
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0054.map.gz / Format: CCP4 / Size: 512 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 512 pix.
= 545.28 Å
1.07 Å/pix.
x 512 pix.
= 545.28 Å
1.07 Å/pix.
x 512 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 LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.25493634 - 0.45862737
Average (Standard dev.)0.0027425927 (±0.027666343)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 545.28 Å
α=β=γ: 90.0 °

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
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

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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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