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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 datasharpened map
Sample
  • Virus: Broad bean stain virus
    • Protein or peptide: Large coat-protein subunit
    • Protein or peptide: Small coat-protein subunit
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / membrane => GO:0016020 / structural molecule activity / GTP binding / DNA binding / RNA binding
Similarity search - Function
Large coat protein / RNA2 polyprotein / Large coat protein / Small coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Genome polyprotein M
Similarity search - Component
Biological speciesBroad 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
Funding supportNew Caledonia, France, 3 items
OrganizationGrant numberCountry
Government of New CaledoniaNew Caledonia
France BioImaging (FBI)ANR-10-INBS-04-01 France
French Infrastructure for Integrated Structural BiologyANR-10-INBS-05 France
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.
History
DepositionDec 27, 2018-
Header (metadata) releaseJan 9, 2019-
Map releaseMay 1, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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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 modelsPDB-6qcc
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4504.png

Downloads & links

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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)
Annotationsharpened map
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.202414 - 0.29871136
Average (Standard dev.)0.00017448509 (±0.013553439)
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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Additional map: unsharpened map

Fileemd_4504_additional.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_4504_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_4504_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Broad bean stain virus

EntireName: Broad bean stain virus
Components
  • Virus: Broad bean stain virus
    • Protein or peptide: Large coat-protein subunit
    • Protein or peptide: Small coat-protein subunit

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Supramolecule #1: Broad bean stain virus

SupramoleculeName: Broad bean stain virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 593572 / Sci species name: Broad bean stain virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Vicia faba (fava bean)
Virus shellShell ID: 1 / Name: capsid / Diameter: 300.0 Å / T number (triangulation number): 1

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Macromolecule #1: Large coat-protein subunit

MacromoleculeName: Large coat-protein subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Broad bean stain virus
Molecular weightTheoretical: 41.247977 KDa
SequenceString: MDVDLFKLSL DDTSSVKGSL LDTRFAQVRV VIPKAMAGGN ELLNSNLYDI LVVDNNFRAA AALAHTHIIE GQIKCVCTIN LPENTGCCL ALCVNSSNRG QFSTDIYTIG SQDRMLWNPA CSKNSTFTFN PNPCGTGWSL EFLRRTKFHI SVVCVSGWSA Q PQTDLVMT ...String:
MDVDLFKLSL DDTSSVKGSL LDTRFAQVRV VIPKAMAGGN ELLNSNLYDI LVVDNNFRAA AALAHTHIIE GQIKCVCTIN LPENTGCCL ALCVNSSNRG QFSTDIYTIG SQDRMLWNPA CSKNSTFTFN PNPCGTGWSL EFLRRTKFHI SVVCVSGWSA Q PQTDLVMT MDFFVANVPC VPRIYNLGSP GQTLWLNRWM GKLSFGQGVS NDIKSMPLAI GGGAGAKDSI LMNMTNAYLS LW RYFHGDL VFEVNKMSSP YIKSTVTFFI GFGGVSFQPE LEDFPNKLVQ FSEVQEKIEL KFTRAEFLTA WSTQVDPAAQ LAN DGCPYL YAMVHDSTAS TIVGDFNLGV TLTRIENFAG IGCNPGIQGA RLLGSAIATP Q

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Macromolecule #2: Small coat-protein subunit

MacromoleculeName: Small coat-protein subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Broad bean stain virus
Molecular weightTheoretical: 23.589662 KDa
SequenceString: NAVVRSSPGI YSNCFSLRAP LKPDGPKSFT CDLMGGGVVT DGDTGWQVTV RNTPVSNLLR TAAWKRGTVH VQVVLAGASV KRSDWDSTV QIFLRQSMAT SSYDAKIWDI CQPGAAMLEF SFDVVGPNSG FEMWDSNWAS QTSWFLEFLI SNPAQNTLFE V NLRLDENF ...String:
NAVVRSSPGI YSNCFSLRAP LKPDGPKSFT CDLMGGGVVT DGDTGWQVTV RNTPVSNLLR TAAWKRGTVH VQVVLAGASV KRSDWDSTV QIFLRQSMAT SSYDAKIWDI CQPGAAMLEF SFDVVGPNSG FEMWDSNWAS QTSWFLEFLI SNPAQNTLFE V NLRLDENF SVAGTTLMPP FVLDRVSVAR PLLGKQTKTV ARSARVVRET KEASESP

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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

Concentration2 mg/mL
BufferpH: 7.4 / Component - Concentration: 20.0 mM / Component - Formula: K2HPO4/KH2PO4 / Component - Name: Phosphate
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 298.15 K / Instrument: GATAN CRYOPLUNGE 3 / Details: blot for 1 second before plunging.

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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 / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 3-9 / Number grids imaged: 1 / Number real images: 2899 / Average exposure time: 2.0 sec. / Average electron dose: 45.0 e/Å2 / Details: 1494 images were retained for 3D reconstruction
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 35663
CTF correctionSoftware:
Namedetails
Gctf (ver. 1.06)CTF calculation
RELION (ver. 3.0-beta-2)CTF correction
Startup modelType of model: INSILICO MODEL / In silico model: Generated by RELION
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0-beta-2)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0-beta-2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0-beta-2)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0-beta-2) / Number images used: 17233
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1ny7

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6qcc:
Cryo-EM Atomic Structure of Broad Bean Stain Virus (BBSV)

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