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- EMDB-41301: Zophobas morio black wasting virus strain OR-molitor virion structure -

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Basic information

Entry
Database: EMDB / ID: EMD-41301
TitleZophobas morio black wasting virus strain OR-molitor virion structure
Map dataMain cyoEM map
Sample
  • Virus: Zophobas morio densovirus
    • Protein or peptide: Major capsid protein
    • DNA: DNA (5'-D(P*CP*G)-3')
    • DNA: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3')
    • DNA: DNA (5'-D(P*TP*CP*GP*AP*A)-3')
KeywordsCapsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA / VIRUS / VIRUS-DNA complex
Biological speciesTenebrio molitor (yellow mealworm) / Zophobas morio densovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsPenzes JJ / Kaelber JT
Funding support United States, 2 items
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 JJ / Holm M / Firlar E / Kaelber JT
History
DepositionJul 20, 2023-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41301.png

Downloads & links

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Map

FileDownload / File: emd_41301.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain cyoEM map
Voxel sizeX=Y=Z: 0.63 Å
Density
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.019058693 - 0.03715192
Average (Standard dev.)0.00012647444 (±0.001943656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions810810810
Spacing810810810
CellA=B=C: 510.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41301_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41301_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Zophobas morio densovirus

EntireName: Zophobas morio densovirus
Components
  • Virus: Zophobas morio densovirus
    • Protein or peptide: Major capsid protein
    • DNA: DNA (5'-D(P*CP*G)-3')
    • DNA: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3')
    • DNA: DNA (5'-D(P*TP*CP*GP*AP*A)-3')

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Supramolecule #1: Zophobas morio densovirus

SupramoleculeName: Zophobas morio densovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified from asymptomatic T. molitor larvae / NCBI-ID: 2750924 / Sci species name: Zophobas morio densovirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Zophobas morio (beetle)
Virus shellShell ID: 1 / Diameter: 28.0 Å / T number (triangulation number): 1

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tenebrio molitor (yellow mealworm)
Molecular weightTheoretical: 48.114625 KDa
SequenceString: ATAILRPIGL HVEKFQQTYR KKWRFLTSAN ANVILAEAAS GERPARWALT TGMASIPWEY LFFYMSPAEY NRMKNYPGTF AKSASVRIR TWNTRVAFQT GDTQTANATL NQNKFLQVAK GIRSIPFICS TNRKYTYSDT EPMQPTGFAT LTSYEYRDGL K TAMYGYDN ...String:
ATAILRPIGL HVEKFQQTYR KKWRFLTSAN ANVILAEAAS GERPARWALT TGMASIPWEY LFFYMSPAEY NRMKNYPGTF AKSASVRIR TWNTRVAFQT GDTQTANATL NQNKFLQVAK GIRSIPFICS TNRKYTYSDT EPMQPTGFAT LTSYEYRDGL K TAMYGYDN DNKDFAKKPP ADATGAEIYL QDYLTIYTND ARATTGTKIL AGFPPYKNFI EEFDASACIN TDVVAMDYDF SY APLVPQF APVPNNLITQ NYNGSYPAGT KNEVTAAKTT DSSQATAPTQ VRNAPRKYIQ GPHADTTFFD EEQNYLRVPI EQG GIFEEV NVETVHDTQM PSINVGIRAV PKLTTIDETT QANSWLDAQG YFEVDCVLTT ESVDPYTYIK GGCYSANTKS QLQY FASDG RPIAKVYDNP NVYGRMQMIK TVKP

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Macromolecule #2: DNA (5'-D(P*CP*G)-3')

MacromoleculeName: DNA (5'-D(P*CP*G)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Tenebrio molitor (yellow mealworm)
Molecular weightTheoretical: 573.43 Da
SequenceString:
(DC)(DG)

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Macromolecule #3: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Tenebrio molitor (yellow mealworm)
Molecular weightTheoretical: 2.733827 KDa
SequenceString:
(DC)(DA)(DG)(DG)(DC)(DC)(DA)(DA)(DA)

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Macromolecule #4: DNA (5'-D(P*TP*CP*GP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*TP*CP*GP*AP*A)-3') / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Tenebrio molitor (yellow mealworm)
Molecular weightTheoretical: 1.504037 KDa
SequenceString:
(DT)(DC)(DG)(DA)(DA)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4 / Component - Formula: PBS / Component - Name: Phosphate-buffered saline
GridSupport film - Material: GOLD / Support film - topology: HOLEY / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified virus from homogenized T. molitor larval tissue

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 3.0 sec. / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 151035
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio 3D model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 8130
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM (ver. 4.0)
Final 3D classificationNumber classes: 35 / Software - Name: cisTEM
Details: Particles were differentiated from the empty capsid population by 2D classification

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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