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- EMDB-41125: Zophobas morio black wasting virus strain NJ2-molitor virion structure -
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Open data
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Basic information
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Title | Zophobas morio black wasting virus strain NJ2-molitor virion structure | |||||||||
![]() | Main map | |||||||||
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![]() | Capsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA / VIRUS / VIRUS-DNA complex | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.0 Å | |||||||||
![]() | Penzes JJ / Kaelber JT | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.6 GB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.3 KB 19.3 KB | Display Display | ![]() |
Images | ![]() | 82 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 2.5 GB 2.5 GB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 33.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8t9xMC ![]() 8t9cC ![]() 8t9eC ![]() 8ta7C ![]() 8tjeC M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.63 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map of D 1000275531 em-volume P1.map.V3
File | emd_41125_half_map_1.map | ||||||||||||
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Annotation | Half map of D_1000275531_em-volume_P1.map.V3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of D 1000275531 em-volume P1.map.V3
File | emd_41125_half_map_2.map | ||||||||||||
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Annotation | Half map of D_1000275531_em-volume_P1.map.V3 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Zophobas morio densovirus
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Zophobas morio densovirus
Supramolecule | Name: 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 |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Diameter: 28.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Major capsid protein
Macromolecule | Name: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 48.085629 KDa |
Sequence | String: 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 |
-Macromolecule #2: DNA (5'-D(P*CP*GP*A)-3')
Macromolecule | Name: DNA (5'-D(P*CP*GP*A)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 886.637 Da |
Sequence | String: (DC)(DG)(DA) |
-Macromolecule #3: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3')
Macromolecule | Name: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*AP*A)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 2.733827 KDa |
Sequence | String: (DC)(DA)(DG)(DG)(DC)(DC)(DA)(DA)(DA) |
-Macromolecule #4: DNA (5'-D(P*TP*CP*GP*AP*A)-3')
Macromolecule | Name: DNA (5'-D(P*TP*CP*GP*AP*A)-3') / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.504037 KDa |
Sequence | String: (DT)(DC)(DG)(DA)(DA) |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 80 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 1.0 x / Component - Formula: PBS / Component - Name: Phosphate-buffered saline |
Grid | Model: 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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
Details | Purified virus from homogenized T. molitor larval tissue |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film 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 beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8t9x: |