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- PDB-8eu5: Acheta domesticus segmented densovirus high buoyancy fraction 2 e... -

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Basic information

Entry
Database: PDB / ID: 8eu5
TitleAcheta domesticus segmented densovirus high buoyancy fraction 2 empty capsid structure
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / parvovirus / densovirus / virus capsid / virion / insect virus / capsid / invertebrate / virus
Function / homologyCapsid protein
Function and homology information
Biological speciesSolenopsis invicta-associated densovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsPenzes, J.J. / McKenna, R. / Tijssen, P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
National Institutes of Health/Office of the DirectorOD018142 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)RR025080 United States
CitationJournal: To Be Published
Title: Structural and molecular biology of Acheta domesticus segmented densovirus, the first parvovirus to harbor a bipartite genome
Authors: Penzes, J.J. / Pham, H.T. / Chipman, P. / Smith, E. / McKenna, R. / Tijssen, P.
History
DepositionOct 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Jun 19, 2024Group: Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein


Theoretical massNumber of molelcules
Total (without water)36,2921
Polymers36,2921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Capsid protein


Mass: 36291.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solenopsis invicta-associated densovirus
Gene: CP / Production host: Acheta domesticus (house cricket) / References: UniProt: A0A891H5C3

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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: unclassified Densovirinae / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: unclassified Densovirinae (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Virus shellDiameter: 210 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4
Buffer componentConc.: 1 x / Name: Phosphate-buffered saline
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Deceased common house crickets, previously showing signs of paralysis, inability to jump, and inability to control movement
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 4320 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsPhase plate: VOLTA PHASE PLATE

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Processing

SoftwareName: PHENIX / Version: 1.10_2155: / Classification: refinement
EM software
IDNameVersionCategory
7UCSF Chimera1.13.1model fitting
13Coot0.8.9.3model refinement
14PHENIX1.10.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 58680
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48354 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009307920
ELECTRON MICROSCOPYf_angle_d0.693556620
ELECTRON MICROSCOPYf_dihedral_angle_d17.27159060
ELECTRON MICROSCOPYf_chiral_restr0.05324360
ELECTRON MICROSCOPYf_plane_restr0.00448060

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