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- EMDB-4504: Cryo-EM Atomic Structure of Broad Bean Stain Virus (BBSV) -

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Basic information

Entry
Database: EMDB / ID: EMD-4504
TitleCryo-EM Atomic Structure of Broad Bean Stain Virus (BBSV)
Map data
SampleBroad 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
Polyprotein
SourceBroad bean stain virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsLecorre F / Lai Jee Him J / Blanc S / Zeddam J-L / Trapani S / Bron P
CitationJournal: 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 ReportPDB-ID: 6qcc

SummaryFull reportAbout validation report
DateDeposition: Dec 27, 2018 / Header (metadata) release: Jan 9, 2019 / Map release: May 1, 2019 / Update: May 1, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6qcc
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6qcc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_4504.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 500 pix.
= 555. Å
1.11 Å/pix.
x 500 pix.
= 555. Å
1.11 Å/pix.
x 500 pix.
= 555. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.013489549 - 0.047537427
Average (Standard dev.)0.00017595381 (±0.0037942673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 555.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z555.000555.000555.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.2020.2990.000

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Supplemental data

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Sample components

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Entire Broad bean stain virus

EntireName: Broad bean stain virus / Number of components: 3

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Component #1: virus, Broad bean stain virus

VirusName: Broad bean stain virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Broad bean stain virus
Source (natural)Host Species: Vicia faba (fava bean)
Shell #1Name of element: capsid / Diameter: 300.0 Å / T number (triangulation number): 1

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Component #2: protein, Large coat-protein subunit

ProteinName: Large coat-protein subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.247977 kDa
SourceSpecies: Broad bean stain virus

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Component #3: protein, Small coat-protein subunit

ProteinName: Small coat-protein subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.589662 kDa
SourceSpecies: Broad bean stain virus

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL / pH: 7.4
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 298.15 K / Humidity: 99 % / Details: blot for 1 second before plunging.

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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: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000.0 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2899 / Sampling size: 14 µm / Details: 1494 images were retained for 3D reconstruction

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 17233
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 1NY7
Output model

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