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- PDB-8t9x: Zophobas morio black wasting virus strain NJ2-molitor virion structure -

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Basic information

Entry
Database: PDB / ID: 8t9x
TitleZophobas morio black wasting virus strain NJ2-molitor virion structure
Components
  • DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3')
  • DNA (5'-D(P*CP*GP*A)-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 speciesZophobas morio black wasting virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 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 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Source and taxonomy / Category: entity_src_nat
Item: _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific

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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*GP*A)-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)53,2104
Polymers53,2104
Non-polymers00
Water1,44180
1
A: Major capsid protein
B: DNA (5'-D(P*CP*GP*A)-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)3,192,608240
Polymers3,192,608240
Non-polymers00
Water2,162120
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
B: DNA (5'-D(P*CP*GP*A)-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 5


  • icosahedral pentamer
  • 266 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)266,05120
Polymers266,05120
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein
B: DNA (5'-D(P*CP*GP*A)-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 6


  • icosahedral 23 hexamer
  • 319 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)319,26124
Polymers319,26124
Non-polymers00
Water21612
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: 48085.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zophobas morio black wasting virus
#2: DNA chain DNA (5'-D(P*CP*GP*A)-3')


Mass: 886.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zophobas morio black wasting virus
#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) Zophobas morio black wasting virus
#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) Zophobas morio black wasting virus
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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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 T. molitor larvae, which were asymptomatic
Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Zophobas morio densovirus / Strain: NJ2-molitor
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Tenebrio molitor
Virus shellDiameter: 28 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4
Buffer componentConc.: 1 x / 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 FIELDBright-field microscopy / 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: 32 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
1cryoSPARCparticle selection
2SerialEM3.8image acquisition
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 156329
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15964 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008208737
ELECTRON MICROSCOPYf_angle_d0.745284815
ELECTRON MICROSCOPYf_dihedral_angle_d5.56328500
ELECTRON MICROSCOPYf_chiral_restr0.04631141
ELECTRON MICROSCOPYf_plane_restr0.00737378

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