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- EMDB-41106: Zophobas morio black wasting virus strain UT-morio virion structure -

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Basic information

Entry
Database: EMDB / ID: EMD-41106
TitleZophobas morio black wasting virus strain UT-morio virion structure
Map dataZophobas morio black wasting virus UT-morio strain, capsid structure of mature virions
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*A)-3')
    • DNA: DNA (5'-D(P*CP*GP*A)-3')
KeywordsCapsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA / VIRUS / VIRUS-DNA complex
Biological speciesZophobas morio (beetle) / Zophobas morio densovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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
DepositionJun 23, 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_41106.png

Downloads & links

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Map

FileDownload / File: emd_41106.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationZophobas morio black wasting virus UT-morio strain, capsid structure of mature virions
Voxel sizeX=Y=Z: 1.011 Å
Density
Contour LevelBy AUTHOR: 0.0261
Minimum - Maximum-0.04409496 - 0.12921801
Average (Standard dev.)0.0012053732 (±0.008476128)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 452.928 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41106_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_41106_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*A)-3')
    • DNA: DNA (5'-D(P*CP*GP*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 Z. morio larvae displaying symptomes of Zophobas morio black wasting disease
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: Zophobas morio (beetle)
Molecular weightTheoretical: 65.638352 KDa
SequenceString: MPRVRPLGPN PQDRPNWDSM NDGQRRYAME QWNLARVRRG EYFDPPGDDD LPLTQADAID NFDLDLLGSP QEAEQPSQQS EDGVDDFLQ QVRDRQDLRD AGPSNAPQPN MADVEMAQVS SSSSGSKRGS DGSGPPSKVS KSGTSLPGTG GNLDGMARGG S GEGGATAI ...String:
MPRVRPLGPN PQDRPNWDSM NDGQRRYAME QWNLARVRRG EYFDPPGDDD LPLTQADAID NFDLDLLGSP QEAEQPSQQS EDGVDDFLQ QVRDRQDLRD AGPSNAPQPN MADVEMAQVS SSSSGSKRGS DGSGPPSKVS KSGTSLPGTG GNLDGMARGG S GEGGATAI LRPIGLHVEK FQQTYRKKWR FLTSANANVI LAEAASGERP ARWALTTGMA SIPWEYLFFY MSPAEYNRMK NY PGTFAKS ASVRIRTWNT RVAFQTGDTQ TANATLNQNK FLQVAKGIRS IPFICSTNRK YTYSDTEPMQ PTGFATLTSY EYR DGLKIA MYGYDNDSPD FAKKPPADAT GAEIYLQDYL TIYTNDARAT TGTKILAGFP PYKNFIEEFD ASACINTDVV AMDY DFSYA PLVPQFAPVP NNLITQNYNA SYPAGTKNEV TAAKTTDSSQ ATPPTQVRNA PRKYIQGPNA DTTFFDEEQN YLRVP IEQG GIFEEVNVET VHDTQMPSIN VGIRAVPKLT TIDETTQANS WLDAQGYFEV DCVLTTESVD PYTYIKGGCY SANTKS QLQ YFANDGRPIA KVYDNPNVYG RMQMIKTVKP

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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: Zophobas morio (beetle)
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*A)-3')

MacromoleculeName: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*A)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Zophobas morio (beetle)
Molecular weightTheoretical: 2.42062 KDa
SequenceString:
(DC)(DA)(DG)(DG)(DC)(DC)(DA)(DA)

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

MacromoleculeName: DNA (5'-D(P*CP*GP*A)-3') / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Zophobas morio (beetle)
Molecular weightTheoretical: 886.637 Da
SequenceString:
(DC)(DG)(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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsPurified virus from homogenized Z. morio larval tissue

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 43.16 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 93965
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio 3D model
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM
Final 3D classificationNumber classes: 35 / Software - Name: cisTEM
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0)
Final reconstructionNumber classes used: 10 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 42219

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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