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- PDB-8eu7: Acheta domesticus segmented densovirus VP-ORF1 virus-like particle -

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Basic information

Entry
Database: PDB / ID: 8eu7
TitleAcheta domesticus segmented densovirus VP-ORF1 virus-like particle
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: 3.3 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: Nat Commun / Year: 2023
Title: Bipartite genome and structural organization of the parvovirus Acheta domesticus segmented densovirus.
Authors: Judit J Pénzes / Hanh T Pham / Paul Chipman / Emmanuel W Smith / Robert McKenna / Peter Tijssen /
Abstract: Parvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression ...Parvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression cassettes within their genome. We report the discovery of a parvovirus with a bipartite genome, Acheta domesticus segmented densovirus (AdSDV), isolated from house crickets (Acheta domesticus), in which it is pathogenic. We found that the AdSDV harbors its NS and VP cassettes on two separate genome segments. Its vp segment acquired a phospholipase A2-encoding gene, vpORF3, via inter-subfamily recombination, coding for a non-structural protein. We showed that the AdSDV evolved a highly complex transcription profile in response to its multipartite replication strategy compared to its monopartite ancestors. Our structural and molecular examinations revealed that the AdSDV packages one genome segment per particle. The cryo-EM structures of two empty- and one full-capsid population (3.3, 3.1 and 2.3 Å resolution) reveal a genome packaging mechanism, which involves an elongated C-terminal tail of the VP, "pinning" the ssDNA genome to the capsid interior at the twofold symmetry axis. This mechanism fundamentally differs from the capsid-DNA interactions previously seen in parvoviruses. This study provides new insights on the mechanism behind ssDNA genome segmentation and on the plasticity of parvovirus biology.
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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_struct_assembly
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_assembly.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
A: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)2,177,51460
Polymers2,177,51460
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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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: RECOMBINANT
Source (natural)Organism: unclassified Densovirinae (virus)
Source (recombinant)Organism: Autographa californica multiple nucleopolyhedrovirus
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Acheta domesticus
Virus shellDiameter: 210 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4
Buffer componentConc.: 1 x / Name: Phosphate-buffered saline
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Recombinantly expressed by the Bac-to-Bac expression system, purified on a sucrose step gradient
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: 2570 nm / Nominal defocus min: 570 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1700
EM imaging opticsPhase plate: VOLTA PHASE PLATE

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Processing

SoftwareName: PHENIX / Version: 1.10_2155: / Classification: refinement
EM software
IDNameVersionCategory
1cisTEM1.0.0particle selection
4CTFFIND4CTF correction
7UCSF Chimera1.13.1model fitting
9Coot0.8.9.3model refinement
10PHENIX1.10.1model refinement
13cisTEM1.0.0classification
14cisTEM1.0.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 18598
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13019 / Num. of class averages: 8 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009307920
ELECTRON MICROSCOPYf_angle_d0.723556620
ELECTRON MICROSCOPYf_dihedral_angle_d17.45159060
ELECTRON MICROSCOPYf_chiral_restr0.05424360
ELECTRON MICROSCOPYf_plane_restr0.00448060

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