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

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Basic information

Entry
Database: PDB / ID: 6qcc
TitleCryo-EM Atomic Structure of Broad Bean Stain Virus (BBSV)
Components
  • Large coat-protein subunit
  • Small coat-protein subunit
KeywordsVIRUS / comovirus capsid plant virus BBSV
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / symbiont-mediated suppression of host innate immune response / GTP binding / structural molecule activity / DNA binding / RNA binding / membrane
Similarity search - Function
Large coat protein / RNA2 polyprotein / Large coat protein / Small coat protein / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBroad bean stain virus
MethodELECTRON MICROSCOPY / single 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, 3items
OrganizationGrant numberCountry
Government of New CaledoniaNew Caledonia
French Infrastructure for Integrated Structural BiologyANR-10-INBS-05 France
France BioImaging (FBI)ANR-10-INBS-04-01 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, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionMay 1, 2019ID: 5NPX
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-4504
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Large coat-protein subunit
B: Small coat-protein subunit


Theoretical massNumber of molelcules
Total (without water)64,8382
Polymers64,8382
Non-polymers00
Water00
1
A: Large coat-protein subunit
B: Small coat-protein subunit
x 60


Theoretical massNumber of molelcules
Total (without water)3,890,258120
Polymers3,890,258120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Large coat-protein subunit
B: Small coat-protein subunit
x 5


  • icosahedral pentamer
  • 324 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)324,18810
Polymers324,18810
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Large coat-protein subunit
B: Small coat-protein subunit
x 6


  • icosahedral 23 hexamer
  • 389 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)389,02612
Polymers389,02612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Large coat-protein subunit


Mass: 41247.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Broad bean stain virus / References: UniProt: D0PSV7
#2: Protein Small coat-protein subunit


Mass: 23589.662 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Broad bean stain virus / References: UniProt: D0PSV7

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Broad bean stain virus / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Broad bean stain virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Vicia faba
Virus shellName: capsid / Diameter: 300 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4
Buffer componentConc.: 20 mM / Name: Phosphate / Formula: K2HPO4/KH2PO4
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 298.15 K / Details: blot for 1 second before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 45 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2899 / Details: 1494 images were retained for 3D reconstruction
Image scansSampling size: 14 µm / Width: 2048 / Height: 2048 / Movie frames/image: 35 / Used frames/image: 3-9

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Processing

EM software
IDNameVersionCategoryDetails
1Gautomatch0.53particle selection
2EPUimage acquisition
4Gctf1.06CTF correctionCTF calculation
5RELION3.0-beta-2CTF correctionCTF correction
8SUPERmodel fittingProgram by Jorge Navaza
9Coot0.8.3model fitting
11RELION3.0-beta-2initial Euler assignment
12RELION3.0-beta-2final Euler assignment
13RELION3.0-beta-2classification
14RELION3.0-beta-23D reconstruction
15PHENIX1.14-3260model refinement
16Coot0.8.9.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 35663
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17233 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 1NY7

1ny7


Accession code: 1NY7 / Source name: PDB / Type: experimental model

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