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Yorodumi- EMDB-41131: Zophobas morio black wasting virus strain OR-molitor empty capsid... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41131 | |||||||||
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Title | Zophobas morio black wasting virus strain OR-molitor empty capsid structure | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Capsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA / VIRUS | |||||||||
Biological species | Tenebrio molitor (yellow mealworm) / Zophobas morio densovirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 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_41131.map.gz | 1.8 GB | EMDB map data format | |
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Header (meta data) | emd-41131-v30.xml emd-41131.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_41131.png | 84.5 KB | ||
Filedesc metadata | emd-41131.cif.gz | 5.9 KB | ||
Others | emd_41131_half_map_1.map.gz emd_41131_half_map_2.map.gz | 1.6 GB 1.6 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41131 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41131 | HTTPS FTP |
-Validation report
Summary document | emd_41131_validation.pdf.gz | 1004.3 KB | Display | EMDB validaton report |
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Full document | emd_41131_full_validation.pdf.gz | 1003.9 KB | Display | |
Data in XML | emd_41131_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | emd_41131_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41131 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41131 | HTTPS FTP |
-Related structure data
Related structure data | 8ta7MC 8t9cC 8t9eC 8t9xC 8tjeC 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_41131.map.gz / Format: CCP4 / Size: 2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.627 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_41131_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41131_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: Yes |
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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: 65.596359 KDa |
Sequence | String: 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 |
-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 | Model: 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 |
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-8ta7: |