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Yorodumi- EMDB-41301: Zophobas morio black wasting virus strain OR-molitor virion structure -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41301 | |||||||||
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Title | Zophobas morio black wasting virus strain OR-molitor virion structure | |||||||||
Map data | Main cyoEM map | |||||||||
Sample |
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Keywords | Capsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA / VIRUS / VIRUS-DNA complex | |||||||||
Biological species | Tenebrio molitor (yellow mealworm) / Zophobas morio densovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Penzes JJ / Kaelber JT | |||||||||
Funding support | United States, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41301.map.gz | 1.8 GB | EMDB map data format | |
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Header (meta data) | emd-41301-v30.xml emd-41301.xml | 18.4 KB 18.4 KB | Display Display | EMDB header |
Images | emd_41301.png | 78.6 KB | ||
Others | emd_41301_half_map_1.map.gz emd_41301_half_map_2.map.gz | 1.6 GB 1.6 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41301 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41301 | HTTPS FTP |
-Validation report
Summary document | emd_41301_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_41301_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_41301_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | emd_41301_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41301 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41301 | HTTPS FTP |
-Related structure data
Related structure data | 8tjeMC 8t9cC 8t9eC 8t9xC 8ta7C M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41301.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Main cyoEM 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: #2
File | emd_41301_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41301_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Zophobas morio densovirus
Entire | Name: Zophobas morio densovirus |
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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: 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 |
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Host (natural) | Organism: Zophobas morio (beetle) |
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: Tenebrio molitor (yellow mealworm) |
Molecular weight | Theoretical: 48.114625 KDa |
Sequence | String: 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 |
-Macromolecule #2: DNA (5'-D(P*CP*G)-3')
Macromolecule | Name: DNA (5'-D(P*CP*G)-3') / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Tenebrio molitor (yellow mealworm) |
Molecular weight | Theoretical: 573.43 Da |
Sequence | String: (DC)(DG) |
-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: Tenebrio molitor (yellow mealworm) |
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: Tenebrio molitor (yellow mealworm) |
Molecular weight | Theoretical: 1.504037 KDa |
Sequence | String: (DT)(DC)(DG)(DA)(DA) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 / Component - Formula: PBS / Component - Name: Phosphate-buffered saline |
Grid | Support film - Material: GOLD / Support film - topology: HOLEY / Details: unspecified |
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 |
-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: 33.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8tje: |