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- PDB-8phh: Cryo-EM structure of Atkinsonella Hypoxylon Virus-like particles. -

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Basic information

Entry
Database: PDB / ID: 8phh
TitleCryo-EM structure of Atkinsonella Hypoxylon Virus-like particles.
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / Partitivirus / plant virus / VLP.
Function / homologyviral capsid / Capsid protein
Function and homology information
Biological speciesAtkinsonella hypoxylon (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsByrne, M.J. / Sainsbury, F.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: Cryo-EM structure of Atkinsonella Hypoxylon Virus-like particles.
Authors: Byrne, M.J. / Sainsbury, F.
History
DepositionJun 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 28, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Capsid protein
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)147,4952
Polymers147,4952
Non-polymers00
Water00
1
B: Capsid protein
A: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)8,849,676120
Polymers8,849,676120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area17150 Å2
ΔGint-89 kcal/mol
Surface area42290 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Capsid protein
A: Capsid protein
x 5


  • icosahedral pentamer
  • 737 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)737,47310
Polymers737,47310
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
B: Capsid protein
A: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 885 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)884,96812
Polymers884,96812
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 Capsid protein / CP / Coat protein


Mass: 73747.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Atkinsonella hypoxylon (fungus) / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q85056
Has protein modificationN

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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: Atkinsonella hypoxylon virus / Type: VIRUS / Details: Virus-like particle expressed in plants. / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Atkinsonella hypoxylon virus
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Atkinsonella hypoxylon
Virus shellDiameter: 380 nm / Triangulation number (T number): 1
Buffer solutionpH: 7
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27700 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0079374
ELECTRON MICROSCOPYf_angle_d0.84212738
ELECTRON MICROSCOPYf_dihedral_angle_d4.2725602
ELECTRON MICROSCOPYf_chiral_restr0.0561412
ELECTRON MICROSCOPYf_plane_restr0.0071638

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