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- EMDB-41125: Zophobas morio black wasting virus strain NJ2-molitor virion structure -

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Basic information

Entry
Database: EMDB / ID: EMD-41125
TitleZophobas morio black wasting virus strain NJ2-molitor virion structure
Map dataMain map
Sample
  • Virus: Zophobas morio densovirus
    • Protein or peptide: Major capsid protein
    • DNA: DNA (5'-D(P*CP*GP*A)-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')
  • Ligand: water
KeywordsCapsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA / VIRUS / VIRUS-DNA complex
Biological speciesZophobas morio black wasting virus / Zophobas morio densovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 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 26, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41125.png

Downloads & links

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Map

FileDownload / File: emd_41125.map.gz / Format: CCP4 / Size: 2.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.63 Å/pix.
x 900 pix.
= 567. Å		0.63 Å/pix.
x 900 pix.
= 567. Å		0.63 Å/pix.
x 900 pix.
= 567. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.63 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168
Minimum - Maximum-0.41199747 - 1.1454877
Average (Standard dev.)-0.0011577177 (±0.04454846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions900900900
Spacing900900900
CellA=B=C: 567.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of D 1000275531 em-volume P1.map.V3

Fileemd_41125_half_map_1.map
AnnotationHalf map of D_1000275531_em-volume_P1.map.V3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of D 1000275531 em-volume P1.map.V3

Fileemd_41125_half_map_2.map
AnnotationHalf map of D_1000275531_em-volume_P1.map.V3
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*GP*A)-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')
  • Ligand: water

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Supramolecule #1: Zophobas morio densovirus

SupramoleculeName: Zophobas morio densovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Purified from T. molitor larvae, which were asymptomatic
NCBI-ID: 2750924 / Sci species name: Zophobas morio densovirus / Sci species strain: NJ2-molitor / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Tenebrio molitor (yellow mealworm)
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 black wasting virus
Molecular weightTheoretical: 48.085629 KDa
SequenceString: ATAILRPIGL HVEKFQQTYR KKWRFLTSAN ANVILAEAAS GERPARWALT TGMASIPWEY LFFYMSPAEY NRMKNYPGTF AKSASVRIR TWNTRVAFQT GDTQTANATL NQNKFLQVAK GIRSIPFICS TNRKYTYSDT EPMQPTGFAT LTSYEYRDGL K IAMYGYDN ...String:
ATAILRPIGL HVEKFQQTYR KKWRFLTSAN ANVILAEAAS GERPARWALT TGMASIPWEY LFFYMSPAEY NRMKNYPGTF AKSASVRIR TWNTRVAFQT GDTQTANATL NQNKFLQVAK GIRSIPFICS TNRKYTYSDT EPMQPTGFAT LTSYEYRDGL K IAMYGYDN DSADFAKKPP ADATGAEIYL QDYLTIYTND ARATTGTKIL AGFPPYKNFI EEFDASACIN TDVVAMDYDF SY APLVPQF APVPNNLITQ NYNASYPAGT KNEVTAVKTT DSSQATPPTQ VRNAPRKYIQ GPNADTTFFD 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*GP*A)-3')

MacromoleculeName: DNA (5'-D(P*CP*GP*A)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Zophobas morio black wasting virus
Molecular weightTheoretical: 886.637 Da
SequenceString:
(DC)(DG)(DA)

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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: Zophobas morio black wasting virus
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: Zophobas morio black wasting virus
Molecular weightTheoretical: 1.504037 KDa
SequenceString:
(DT)(DC)(DG)(DA)(DA)

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 80 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 - Concentration: 1.0 x / 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 / Support film - Film thickness: 20 / 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: 32.0 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: 156329
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio 3D model
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 15964
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 50 / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

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

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