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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 dataIcosahedral reconstruction of feline calicivirus strain F9
Sample
  • Complex: T=3 Icosahedral Capsid.
    • Protein or peptide: VP1
  • Ligand: POTASSIUM IONPotassium
Function / homologyT=3 icosahedral viral capsid / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / cytoplasm / Capsid protein
Function and homology information
Biological speciesFeline calicivirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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.
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
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  • 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

emd_0054.png

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)
AnnotationIcosahedral reconstruction of feline calicivirus strain F9
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.
Components
  • Complex: T=3 Icosahedral Capsid.
    • Protein or peptide: VP1
  • Ligand: POTASSIUM IONPotassium

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Supramolecule #1: T=3 Icosahedral Capsid.

SupramoleculeName: T=3 Icosahedral Capsid. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: T=3 Icosahedral Capsid
Source (natural)Organism: Feline calicivirus
Recombinant expressionOrganism: Felis catus (domestic cat)

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Feline calicivirus
Molecular weightTheoretical: 73.346664 KDa
Recombinant expressionOrganism: Felis catus (domestic cat)
SequenceString: MCSTCANVLK YYNWDPHFRL VIDPNKFLSV GFCDNPLMCC YPELLPEFGT VWDCDQSPLQ IYLESILGDD EWASTYEAID PAVPPMHWD AAGKIFQPHP GVLMHHLIGE VAKAWDPNLP MFRLEADGDG SITAPEQGTP VGGVIAEPSA QMSAAADMAT G KSVDSEWE ...String:
MCSTCANVLK YYNWDPHFRL VIDPNKFLSV GFCDNPLMCC YPELLPEFGT VWDCDQSPLQ IYLESILGDD EWASTYEAID PAVPPMHWD AAGKIFQPHP GVLMHHLIGE VAKAWDPNLP MFRLEADGDG SITAPEQGTP VGGVIAEPSA QMSAAADMAT G KSVDSEWE AFFSFHTSVN WSTSETQGKI LFKQSLGPLL NPYLEHLAKL YVAWSGSIDV RFSISGSGVF GGKLAAIVVP PG VDPVQST SMLQYPHVLF DARQVEPVIF SIPDLRSTLY HLMSDTDTTS LVIMVYNDLI NPYANDSNSS GCIVTVETKP GAD FKFHLL KPPGSMLTHG SVPSDLIPKS SSLWIGNRHW TDITDFVIRP FVFQANRHFD FNQETAGWST PRYRPITITI SEKN GAKLG IGVATDYIVP GIPDGWPDTT IPEKLTPAGD YAITNKSGND ITTAAGYDGA DVIVNNTNFK GMYICGSLQR AWGDK KISN TAFITTATKV DNAIEPSNVI DMTKIAVYQD THVGKEVQTS DDTLSLLGYT GIGEQAIGSD RDRVVRISVL PETGAR GGN HPIFYKNSIK LGYVIRSIDV FNSQILHTSR QLSLNHYLLP PDSFAVYRII DSNGSWFDIG IDSDGFSFVG VSSIGKL EF PLTASYMGIQ LAKIRLASNI RSSMTKL

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.2 / Details: Phosphate buffered saline
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified enveloped virions

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 75000
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 5198 / Average electron dose: 63.0 e/Å2
Details: Each micrograph was recorded as a movie of 50 individual fractions with a total dose of 63 e/angstrom squared
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 59531 / Details: Autopicking in Relion
CTF correctionSoftware - Name: Gctf / Details: CTF correction was implemented through Relion
Startup modelType of model: OTHER
Details: Previously published models calculated at lower resolution.
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 2.1)
Details: Origin and orientation values were determined by 3D auto refine in RELION, assuming full icosahedral symmetry (i.e. with full gold-standard methods).
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 41436
DetailsImages were motion-corrected using motioncor2 Defocus estimation was performed using GCTF
FSC plot (resolution estimation)

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