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- EMDB-41131: Zophobas morio black wasting virus strain OR-molitor empty capsid... -

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Basic information

Entry
Database: EMDB / ID: EMD-41131
TitleZophobas morio black wasting virus strain OR-molitor empty capsid structure
Map data
Sample
  • Virus: Zophobas morio densovirus
    • Protein or peptide: Major capsid protein
KeywordsCapsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA / VIRUS
Biological speciesTenebrio molitor (yellow mealworm) / 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: Cell / Year: 2024
Title: Cryo-EM-based discovery of a pathogenic parvovirus causing epidemic mortality by black wasting disease in farmed beetles.
Authors: Judit J Penzes / Martin Holm / Samantha A Yost / Jason T Kaelber /
Abstract: We use cryoelectron microscopy (cryo-EM) as a sequence- and culture-independent diagnostic tool to identify the etiological agent of an agricultural pandemic. For the past 4 years, American insect- ...We use cryoelectron microscopy (cryo-EM) as a sequence- and culture-independent diagnostic tool to identify the etiological agent of an agricultural pandemic. For the past 4 years, American insect-rearing facilities have experienced a distinctive larval pathology and colony collapse of farmed Zophobas morio (superworm). By means of cryo-EM, we discovered the causative agent: a densovirus that we named Zophobas morio black wasting virus (ZmBWV). We confirmed the etiology of disease by fulfilling Koch's postulates and characterizing strains from across the United States. ZmBWV is a member of the family Parvoviridae with a 5,542 nt genome, and we describe intersubunit interactions explaining its expanded internal volume relative to human parvoviruses. Cryo-EM structures at resolutions up to 2.1 Å revealed single-strand DNA (ssDNA) ordering at the capsid inner surface pinned by base-binding pockets in the capsid inner surface. Also, we demonstrated the prophylactic potential of non-pathogenic strains to provide cross-protection in vivo.
History
DepositionJun 26, 2023-
Header (metadata) releaseAug 2, 2023-
Map releaseAug 2, 2023-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41131.png

Downloads & links

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Map

FileDownload / File: emd_41131.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.63 Å/pix.
x 810 pix.
= 507.87 Å		0.63 Å/pix.
x 810 pix.
= 507.87 Å		0.63 Å/pix.
x 810 pix.
= 507.87 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.627 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0115
Minimum - Maximum-0.022047741 - 0.04598855
Average (Standard dev.)0.000058855145 (±0.0022073828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions810810810
Spacing810810810
CellA=B=C: 507.86996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_41131_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #2

Fileemd_41131_half_map_2.map
Projections & Slices
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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

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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: Yes
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: 65.596359 KDa
SequenceString: MPRVRPLGPN PQDRPNWDSM NEGQRRYAME QWNLARVRRG EYFDPPGDDD LPLTQADAID NFDLDLLGSP QEAEQPSQQS EDGVDDFLQ QVRDRQDLRD AGPSNAPQPN MADIEMSQVS SSSGGSKRGS GGGGPPSKVS KSGTSLPGTG GNLDGMVRGG S GEGGATAI ...String:
MPRVRPLGPN PQDRPNWDSM NEGQRRYAME QWNLARVRRG EYFDPPGDDD LPLTQADAID NFDLDLLGSP QEAEQPSQQS EDGVDDFLQ QVRDRQDLRD AGPSNAPQPN MADIEMSQVS SSSGGSKRGS GGGGPPSKVS KSGTSLPGTG GNLDGMVRGG S GEGGATAI LRPIGLHVEK FQQTYRKKWR FLTSANANVI LAEAASGERP ARWALTTGMA SIPWEYLFFY MSPAEYNRMK NY PGTFAKS ASVRIRTWNT RVAFQTGDTQ TANATLNQNK FLQVAKGIRS IPFICSTNRK YTYSDTEPMQ PTGFATLTSY EYR DGLKTA MYGYDNDNKD FAKKPPADAT GAEIYLQDYL TIYTNDARAT TGTKILAGFP PYKNFIEEFD ASACINTDVV AMDY DFSYA PLVPQFAPVP NNLITQNYNG SYPAGTKNEV TAAKTTDSSQ ATAPTQVRNA PRKYIQGPHA DTTFFDEEQN YLRVP IEQG GIFEEVNVET VHDTQMPSIN VGIRAVPKLT TIDETTQANS WLDAQGYFEV DCVLTTESVD PYTYIKGGCY SANTKS QLQ YFASDGRPIA KVYDNPNVYG RMQMIKTVKP

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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: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Pretreatment - Atmosphere: AIR
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
CTF correctionSoftware - Name: cisTEM / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio 3D model
Final reconstructionNumber classes used: 1 / 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: 47770
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cisTEM
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8ta7:
Zophobas morio black wasting virus strain OR-molitor empty capsid structure

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