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- PDB-8ta7: Zophobas morio black wasting virus strain OR-molitor empty capsid... -

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Basic information

Entry
Database: PDB / ID: 8ta7
TitleZophobas morio black wasting virus strain OR-molitor empty capsid structure
ComponentsMajor capsid protein
KeywordsVIRUS / Capsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA
Biological speciesTenebrio molitor (yellow mealworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsPenzes, J.J. / Kaelber, J.T.
Funding support United States, 2items
OrganizationGrant numberCountry
Other government United States
Other private United States
CitationJournal: Cell / Year: 2024
Title: Cryo-EM-based discovery of a pathogenic parvovirus causing epidemic mortality by black wasting disease in farmed beetles.
Authors: Judit J Penzes / Martin Holm / Samantha A Yost / Jason T Kaelber /
Abstract: We use cryoelectron microscopy (cryo-EM) as a sequence- and culture-independent diagnostic tool to identify the etiological agent of an agricultural pandemic. For the past 4 years, American insect- ...We use cryoelectron microscopy (cryo-EM) as a sequence- and culture-independent diagnostic tool to identify the etiological agent of an agricultural pandemic. For the past 4 years, American insect-rearing facilities have experienced a distinctive larval pathology and colony collapse of farmed Zophobas morio (superworm). By means of cryo-EM, we discovered the causative agent: a densovirus that we named Zophobas morio black wasting virus (ZmBWV). We confirmed the etiology of disease by fulfilling Koch's postulates and characterizing strains from across the United States. ZmBWV is a member of the family Parvoviridae with a 5,542 nt genome, and we describe intersubunit interactions explaining its expanded internal volume relative to human parvoviruses. Cryo-EM structures at resolutions up to 2.1 Å revealed single-strand DNA (ssDNA) ordering at the capsid inner surface pinned by base-binding pockets in the capsid inner surface. Also, we demonstrated the prophylactic potential of non-pathogenic strains to provide cross-protection in vivo.
History
DepositionJun 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
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Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name
Revision 1.3Jul 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)65,5961
Polymers65,5961
Non-polymers00
Water00
1
A: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,935,78260
Polymers3,935,78260
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: Major capsid protein
x 5


  • icosahedral pentamer
  • 328 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)327,9825
Polymers327,9825
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
x 6


  • icosahedral 23 hexamer
  • 394 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)393,5786
Polymers393,5786
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 Major capsid protein


Mass: 65596.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tenebrio molitor (yellow mealworm)
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: Zophobas morio densovirus / Type: VIRUS / Details: Purified from asymptomatic T. molitor larvae / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Zophobas morio densovirus
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Zophobas morio
Virus shellDiameter: 28 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4
Buffer componentUnits: 1x / Name: Phosphate-buffered saline / Formula: PBS
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Purified virus from homogenized T. molitor larval tissue
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 33 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1cisTEMparticle selection
2SerialEM3.8image acquisition
4cisTEMCTF correction
9PHENIXmodel refinement
10cisTEMinitial Euler assignment
11RELION4final Euler assignment
12RELIONclassification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 151035
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47770 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003208984
ELECTRON MICROSCOPYf_angle_d0.588284958
ELECTRON MICROSCOPYf_dihedral_angle_d5.12328601
ELECTRON MICROSCOPYf_chiral_restr0.04431119
ELECTRON MICROSCOPYf_plane_restr0.00537297

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