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- PDB-8tje: Zophobas morio black wasting virus strain OR-molitor virion structure -

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Basic information

Entry
Database: PDB / ID: 8tje
TitleZophobas morio black wasting virus strain OR-molitor virion structure
Components
  • DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3')
  • DNA (5'-D(P*CP*G)-3')
  • DNA (5'-D(P*TP*CP*GP*AP*A)-3')
  • Major capsid protein
KeywordsVIRUS/DNA / Capsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA / VIRUS / VIRUS-DNA complex
Function / homologyDNA
Function and homology information
Biological speciesTenebrio molitor (yellow mealworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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
DepositionJul 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein
B: DNA (5'-D(P*CP*G)-3')
C: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3')
D: DNA (5'-D(P*TP*CP*GP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)52,9264
Polymers52,9264
Non-polymers00
Water00
1
A: Major capsid protein
B: DNA (5'-D(P*CP*G)-3')
C: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3')
D: DNA (5'-D(P*TP*CP*GP*AP*A)-3')
x 60


Theoretical massNumber of molelcules
Total (without water)3,175,555240
Polymers3,175,555240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein Major capsid protein


Mass: 48114.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tenebrio molitor (yellow mealworm)
#2: DNA chain DNA (5'-D(P*CP*G)-3')


Mass: 573.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tenebrio molitor (yellow mealworm)
#3: DNA chain DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3')


Mass: 2733.827 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tenebrio molitor (yellow mealworm)
#4: DNA chain DNA (5'-D(P*TP*CP*GP*AP*A)-3')


Mass: 1504.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tenebrio molitor (yellow mealworm)

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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: 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 T. molitor 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: 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
10cisTEMinitial Euler assignment
11cisTEM4final Euler assignment
12cisTEMclassification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 151035
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8130 / 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_d0.002208680
ELECTRON MICROSCOPYf_angle_d0.479284520
ELECTRON MICROSCOPYf_dihedral_angle_d4.19528500
ELECTRON MICROSCOPYf_chiral_restr0.04131080
ELECTRON MICROSCOPYf_plane_restr0.00437260

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