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- EMDB-1942: Feline Calicivirus strain F9 -

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Basic information

Entry
Database: EMDB / ID: EMD-1942
TitleFeline Calicivirus strain F9
Map dataThree-dimensional reconstruction of Feline Calicivirus strain f9 at 9 Angstroms resolution
Sample
  • Sample: Feline Calicivirus
  • Virus: Feline calicivirus
Keywordsfeline / calicivirus / virus / virion
Biological speciesFeline calicivirus
Methodsingle particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsBhella D / Goodfellow IG
CitationJournal: J Virol / Year: 2011
Title: The cryo-electron microscopy structure of feline calicivirus bound to junctional adhesion molecule A at 9-angstrom resolution reveals receptor-induced flexibility and two distinct ...Title: The cryo-electron microscopy structure of feline calicivirus bound to junctional adhesion molecule A at 9-angstrom resolution reveals receptor-induced flexibility and two distinct conformational changes in the capsid protein VP1.
Authors: David Bhella / Ian G Goodfellow /
Abstract: Caliciviridae are small icosahedral positive-sense RNA-containing viruses and include the human noroviruses, a leading cause of infectious acute gastroenteritis and feline calicivirus (FCV), which ...Caliciviridae are small icosahedral positive-sense RNA-containing viruses and include the human noroviruses, a leading cause of infectious acute gastroenteritis and feline calicivirus (FCV), which causes respiratory illness and stomatitis in cats. FCV attachment and entry is mediated by feline junctional adhesion molecule A (fJAM-A), which binds to the outer face of the capsomere, inducing a conformational change in the capsid that may be important for viral uncoating. Here we present the results of our structural investigation of the virus-receptor interaction and ensuing conformational changes. Cryo-electron microscopy and three-dimensional image reconstruction were used to solve the structure of the virus decorated with a soluble fragment of the receptor at subnanometer resolution. In initial reconstructions, the P domains of the capsid protein VP1 and fJAM-A were poorly resolved. Sorting experiments led to improved reconstructions of the FCV-fJAM-A complex both before and after the induced conformational change, as well as in three transition states. These data showed that the P domain becomes flexible following fJAM-A binding, leading to a loss of icosahedral symmetry. Furthermore, two distinct conformational changes were seen; an anticlockwise rotation of up to 15° of the P domain was observed in the AB dimers, while tilting of the P domain away from the icosahedral 2-fold axis was seen in the CC dimers. A list of putative contact residues was calculated by fitting high-resolution coordinates for fJAM-A and VP1 to the reconstructed density maps, highlighting regions in both virus and receptor important for virus attachment and entry.
History
DepositionAug 11, 2011-
Header (metadata) releaseAug 12, 2011-
Map releaseAug 22, 2012-
UpdateAug 22, 2012-
Current statusAug 22, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 35.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 35.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1942.jpg

Downloads & links

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Map

FileDownload / File: emd_1942.map.gz / Format: CCP4 / Size: 61.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThree-dimensional reconstruction of Feline Calicivirus strain f9 at 9 Angstroms resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 255 pix.
= 525.3 Å		2.06 Å/pix.
x 255 pix.
= 525.3 Å		2.06 Å/pix.
x 255 pix.
= 525.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 35.700000000000003 / Movie #1: 35.7
Minimum - Maximum-50.872539519999997 - 152.783691409999989
Average (Standard dev.)3.95410562 (±25.02583504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-127-127-127
Dimensions255255255
Spacing255255255
CellA=B=C: 525.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.062.062.06
M x/y/z255255255
origin x/y/z0.0000.0000.000
length x/y/z525.300525.300525.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-127-127-127
NC/NR/NS255255255
D min/max/mean-50.873152.7843.954

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Supplemental data

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Sample components

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Entire : Feline Calicivirus

EntireName: Feline Calicivirus
Components
  • Sample: Feline Calicivirus
  • Virus: Feline calicivirus

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Supramolecule #1000: Feline Calicivirus

SupramoleculeName: Feline Calicivirus / type: sample / ID: 1000 / Oligomeric state: T3 icosahedral capsid / Number unique components: 1
Molecular weightTheoretical: 10.7 MDa

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Supramolecule #1: Feline calicivirus

SupramoleculeName: Feline calicivirus / type: virus / ID: 1 / Name.synonym: Feline calicivirus / NCBI-ID: 11978 / Sci species name: Feline calicivirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Feline calicivirus
Host (natural)Organism: Felis catus (domestic cat) / synonym: VERTEBRATES
Molecular weightTheoretical: 10.7 MDa
Virus shellShell ID: 1 / Name: VP1 / Diameter: 415 Å / T number (triangulation number): 3

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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

BufferpH: 7.4 / Details: PBS
GridDetails: 400 mesh R2/2 C-flat
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: blot for five seconds before plunging

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Electron microscopy

MicroscopeJEOL 2200FS
TemperatureAverage: 97 K
Alignment procedureLegacy - Astigmatism: corrected at 100k times mag in digital micrograph
Specialist opticsEnergy filter - Name: JEOL / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 100000
Sample stageSpecimen holder: Side entry / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: each particle corrected using bsoft
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: em3dr2 / Number images used: 6802

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