|Entry||Database: EMDB / ID: EMD-4504|
|Title||Cryo-EM Atomic Structure of Broad Bean Stain Virus (BBSV)|
|Sample||Broad bean stain virus:|
virus / Large coat-protein subunit / Small coat-protein subunit
|Function / homology|
Function and homology information
transport of virus in host, cell to cell / host cell plasmodesma / viral capsid / structural molecule activity / integral component of membrane
RNA2 polyprotein / Large coat protein / Viral coat protein subunit / Large coat protein / Small coat protein
|Source||Broad bean stain virus|
|Method||single particle reconstruction / cryo EM / Resolution: 3.22 Å|
|Authors||Lecorre F / Lai Jee Him J / Blanc S / Zeddam J-L / Trapani S / Bron P|
|Citation||Journal: Virology / Year: 2019|
Title: The cryo-electron microscopy structure of Broad Bean Stain Virus suggests a common capsid assembly mechanism among comoviruses.
Authors: François Lecorre / Joséphine Lai-Kee-Him / Stéphane Blanc / Jean-Louis Zeddam / Stefano Trapani / Patrick Bron /
Abstract: The Broad bean stain virus (BBSV) is a member of the genus Comovirus infecting Fabaceae. The virus is transmitted through seed and by plant weevils causing severe and widespread disease worldwide. ...The Broad bean stain virus (BBSV) is a member of the genus Comovirus infecting Fabaceae. The virus is transmitted through seed and by plant weevils causing severe and widespread disease worldwide. BBSV has a bipartite, positive-sense, single-stranded RNA genome encapsidated in icosahedral particles. We present here the cryo-electron microscopy reconstruction of the BBSV and an atomic model of the capsid proteins refined at 3.22 Å resolution. We identified residues involved in RNA/capsid interactions revealing a unique RNA genome organization. Inspection of the small coat protein C-terminal domain highlights a maturation cleavage between Leu567 and Leu568 and interactions of the C-terminal stretch with neighbouring small coat proteins within the capsid pentameric turrets. These interactions previously proposed to play a key role in the assembly of the Cowpea mosaic virus suggest a common capsid assembly mechanism throughout all comovirus species.
|Validation Report||PDB-ID: 6qcc|
SummaryFull reportAbout validation report
|Date||Deposition: Dec 27, 2018 / Header (metadata) release: Jan 9, 2019 / Map release: May 1, 2019 / Update: May 1, 2019|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_4504.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.11 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Broad bean stain virus
|Entire||Name: Broad bean stain virus / Number of components: 3|
-Component #1: virus, Broad bean stain virus
|Virus||Name: Broad bean stain virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: Broad bean stain virus|
|Source (natural)||Host Species: Vicia faba (fava bean)|
|Shell #1||Name of element: capsid / Diameter: 300.0 Å / T number (triangulation number): 1|
-Component #2: protein, Large coat-protein subunit
|Protein||Name: Large coat-protein subunit / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 41.247977 kDa|
|Source||Species: Broad bean stain virus|
-Component #3: protein, Small coat-protein subunit
|Protein||Name: Small coat-protein subunit / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 23.589662 kDa|
|Source||Species: Broad bean stain virus|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 2 mg/mL / pH: 7.4|
|Vitrification||Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298.15 K / Humidity: 99 % / Details: blot for 1 second before plunging.|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 45 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 59000.0 X (nominal) / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Number of digital images: 2899 / Sampling size: 14 µm / Details: 1494 images were retained for 3D reconstruction|
-Atomic model buiding
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