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- EMDB-1945: Feline Calicivirus strain F9 decorated with Junctional Adhesion M... -

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Basic information

Entry
Database: EMDB / ID: EMD-1945
TitleFeline Calicivirus strain F9 decorated with Junctional Adhesion Molecule A
Map dataThree dimensional reconstruction of feline Calicivirus decorated with junctional adhesion molecule A
Sample
  • Sample: Feline Calicivirus decorated with junctional adhesion molecule A
  • Virus: Feline calicivirus
  • Protein or peptide: Junctional Adhesion Molecule A
Keywordsfeline / calicivirus / virus / virion / junctional adhesion molecule
Biological speciesFelis catus (domestic cat) / Feline calicivirus
Methodsingle particle reconstruction / cryo EM / Resolution: 10.2 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-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 44
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 44
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1945.jpg

Downloads & links

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Map

FileDownload / File: emd_1945.map.gz / Format: CCP4 / Size: 49.8 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationThree dimensional reconstruction of feline Calicivirus decorated with junctional adhesion molecule A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 299 pix.
= 615.94 Å		2.06 Å/pix.
x 299 pix.
= 615.94 Å		2.06 Å/pix.
x 299 pix.
= 615.94 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: 44.0 / Movie #1: 44
Minimum - Maximum-366.0 - 427.0
Average (Standard dev.)2.21791291 (±59.512966159999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-149-149-149
Dimensions299299299
Spacing299299299
CellA=B=C: 615.94 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z2.062.062.06
M x/y/z299299299
origin x/y/z0.0000.0000.000
length x/y/z615.940615.940615.940
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-149-149-149
NC/NR/NS299299299
D min/max/mean-366.000427.0002.218

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Supplemental data

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Sample components

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Entire : Feline Calicivirus decorated with junctional adhesion molecule A

EntireName: Feline Calicivirus decorated with junctional adhesion molecule A
Components
  • Sample: Feline Calicivirus decorated with junctional adhesion molecule A
  • Virus: Feline calicivirus
  • Protein or peptide: Junctional Adhesion Molecule A

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Supramolecule #1000: Feline Calicivirus decorated with junctional adhesion molecule A

SupramoleculeName: Feline Calicivirus decorated with junctional adhesion molecule A
type: sample / ID: 1000 / Oligomeric state: T3 icosahedral capsid / Number unique components: 2
Molecular weightTheoretical: 16 MDa

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Supramolecule #1: Feline calicivirus

SupramoleculeName: Feline calicivirus / type: virus / ID: 1 / Name.synonym: FCV / NCBI-ID: 11978 / Sci species name: Feline calicivirus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: FCV
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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Macromolecule #1: Junctional Adhesion Molecule A

MacromoleculeName: Junctional Adhesion Molecule A / type: protein_or_peptide / ID: 1 / Name.synonym: fJAM-A
Details: Virus was incubated in the presence of a soluble fragment of fJAM-A at 4 degrees celsius for one hour.
Number of copies: 180 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Felis catus (domestic cat) / synonym: Domestic cat
Molecular weightTheoretical: 29 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster) / Recombinant plasmid: pDEF:fJAM:Fc

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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: Phosphate Buffered Saline
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 100,000 times magnification 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: 10.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EM3DR2
Details: 12,422 particle images were subjected to a model-based sorting protocol to separate them according to the extent of conformational change they had undergone following fJAM-A binding
Number images used: 3252

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