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- PDB-8t9c: Zophobas morio black wasting virus strain UT-morio virion structure -

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Basic information

Entry
Database: PDB / ID: 8t9c
TitleZophobas morio black wasting virus strain UT-morio virion structure
Components
  • DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*A)-3')
  • DNA (5'-D(P*CP*G)-3')
  • DNA (5'-D(P*CP*GP*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 (beetle)
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: 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 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*A)-3')
D: DNA (5'-D(P*CP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)69,5194
Polymers69,5194
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*A)-3')
D: DNA (5'-D(P*CP*GP*A)-3')
x 60


Theoretical massNumber of molelcules
Total (without water)4,171,142240
Polymers4,171,142240
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)
#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) Zophobas morio (beetle)
#3: DNA chain DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*A)-3')


Mass: 2420.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zophobas morio (beetle)
#4: 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 (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 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 % / 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: 10 sec. / Electron dose: 43.16 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
9cisTEMinitial Euler assignment
10RELION4final Euler assignment
11cisTEMclassification
12RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 93965
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42219 / Algorithm: FOURIER SPACE / Num. of class averages: 10 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003208740
ELECTRON MICROSCOPYf_angle_d0.537284820
ELECTRON MICROSCOPYf_dihedral_angle_d5.3128500
ELECTRON MICROSCOPYf_chiral_restr0.04331140
ELECTRON MICROSCOPYf_plane_restr0.00437380

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