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Yorodumi- EMDB-41106: Zophobas morio black wasting virus strain UT-morio virion structure -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41106 | |||||||||
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Title | Zophobas morio black wasting virus strain UT-morio virion structure | |||||||||
Map data | Zophobas morio black wasting virus UT-morio strain, capsid structure of mature virions | |||||||||
Sample |
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Keywords | Capsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA / VIRUS / VIRUS-DNA complex | |||||||||
Biological species | Zophobas morio (beetle) / 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_41106.map.gz | 320 MB | EMDB map data format | |
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Header (meta data) | emd-41106-v30.xml emd-41106.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
Images | emd_41106.png | 89 KB | ||
Others | emd_41106_half_map_1.map.gz emd_41106_half_map_2.map.gz | 269.7 MB 269.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41106 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41106 | HTTPS FTP |
-Validation report
Summary document | emd_41106_validation.pdf.gz | 912.8 KB | Display | EMDB validaton report |
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Full document | emd_41106_full_validation.pdf.gz | 912.4 KB | Display | |
Data in XML | emd_41106_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | emd_41106_validation.cif.gz | 20.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41106 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41106 | HTTPS FTP |
-Related structure data
Related structure data | 8t9cMC 8t9eC 8t9xC 8ta7C 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_41106.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Zophobas morio black wasting virus UT-morio strain, capsid structure of mature virions | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.011 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_41106_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41106_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 Z. morio larvae displaying symptomes of Zophobas morio black wasting disease 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: Zophobas morio (beetle) |
Molecular weight | Theoretical: 65.638352 KDa |
Sequence | String: MPRVRPLGPN PQDRPNWDSM NDGQRRYAME QWNLARVRRG EYFDPPGDDD LPLTQADAID NFDLDLLGSP QEAEQPSQQS EDGVDDFLQ QVRDRQDLRD AGPSNAPQPN MADVEMAQVS SSSSGSKRGS DGSGPPSKVS KSGTSLPGTG GNLDGMARGG S GEGGATAI ...String: MPRVRPLGPN PQDRPNWDSM NDGQRRYAME QWNLARVRRG EYFDPPGDDD LPLTQADAID NFDLDLLGSP QEAEQPSQQS EDGVDDFLQ QVRDRQDLRD AGPSNAPQPN MADVEMAQVS SSSSGSKRGS DGSGPPSKVS KSGTSLPGTG GNLDGMARGG S GEGGATAI LRPIGLHVEK FQQTYRKKWR FLTSANANVI LAEAASGERP ARWALTTGMA SIPWEYLFFY MSPAEYNRMK NY PGTFAKS ASVRIRTWNT RVAFQTGDTQ TANATLNQNK FLQVAKGIRS IPFICSTNRK YTYSDTEPMQ PTGFATLTSY EYR DGLKIA MYGYDNDSPD FAKKPPADAT GAEIYLQDYL TIYTNDARAT TGTKILAGFP PYKNFIEEFD ASACINTDVV AMDY DFSYA PLVPQFAPVP NNLITQNYNA SYPAGTKNEV TAAKTTDSSQ ATPPTQVRNA PRKYIQGPNA DTTFFDEEQN YLRVP IEQG GIFEEVNVET VHDTQMPSIN VGIRAVPKLT TIDETTQANS WLDAQGYFEV DCVLTTESVD PYTYIKGGCY SANTKS QLQ YFANDGRPIA KVYDNPNVYG RMQMIKTVKP |
-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: Zophobas morio (beetle) |
Molecular weight | Theoretical: 573.43 Da |
Sequence | String: (DC)(DG) |
-Macromolecule #3: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*A)-3')
Macromolecule | Name: DNA (5'-D(P*CP*AP*GP*GP*CP*CP*AP*A)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Zophobas morio (beetle) |
Molecular weight | Theoretical: 2.42062 KDa |
Sequence | String: (DC)(DA)(DG)(DG)(DC)(DC)(DA)(DA) |
-Macromolecule #4: DNA (5'-D(P*CP*GP*A)-3')
Macromolecule | Name: DNA (5'-D(P*CP*GP*A)-3') / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Zophobas morio (beetle) |
Molecular weight | Theoretical: 886.637 Da |
Sequence | String: (DC)(DG)(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 | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 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 Z. morio 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: 10.0 sec. / Average electron dose: 43.16 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-8t9c: |