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- PDB-8t9e: Zophobas morio black wasting virus strain UT-morio empty capsid s... -

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Basic information

Entry
Database: PDB / ID: 8t9e
TitleZophobas morio black wasting virus strain UT-morio empty capsid structure
ComponentsMajor capsid protein
KeywordsVIRUS / Capsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA
Biological speciesZophobas morio (beetle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPenzes, J.J. / Kaelber, J.T.
Funding support United States, 2items
OrganizationGrant numberCountry
Other government United States
Other private United States
CitationJournal: To Be Published
Title: Sequencing-free discovery by cryo-EM of a pathogenic parvovirus causing mass mortality of farmed beetles
Authors: Penzes, J.J. / Holm, M. / Firlar, E. / Kaelber, J.T.
History
DepositionJun 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)65,6381
Polymers65,6381
Non-polymers00
Water00
1
A: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,938,30160
Polymers3,938,30160
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Major capsid protein


Mass: 65638.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zophobas morio (beetle)

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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 Z. morio larvae displaying symptomes of Zophobas morio black wasting disease
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Zophobas morio densovirus
Details of virusEmpty: NO / 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 Z. morio larval tissue
Specimen supportDetails: unspecified
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: 4 sec. / Electron dose: 29 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
10cisTEMinitial Euler assignment
11RELION4final Euler assignment
12cisTEMclassification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 133622
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41960 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005201360
ELECTRON MICROSCOPYf_angle_d0.623274440
ELECTRON MICROSCOPYf_dihedral_angle_d5.4227360
ELECTRON MICROSCOPYf_chiral_restr0.04529820
ELECTRON MICROSCOPYf_plane_restr0.00435880

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