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Yorodumi- EMDB-8753: Multi-membrane Structure of the Pandoravirus and Implications to ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8753 | |||||||||
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Title | Multi-membrane Structure of the Pandoravirus and Implications to Eukaryogenesis | |||||||||
Map data | Cryo-ET Tomogram of P. dulcis | |||||||||
Sample |
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Biological species | Pandoravirus salinus | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Wang KJ / Zhou ZH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: In depth examination of the various structures of P. salinus through CryoET reconstructions Authors: Wang KJ / Zhou ZH | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8753.map.gz | 1.3 GB | EMDB map data format | |
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Header (meta data) | emd-8753-v30.xml emd-8753.xml | 8.2 KB 8.2 KB | Display Display | EMDB header |
Images | emd_8753.png | 92.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8753 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8753 | HTTPS FTP |
-Validation report
Summary document | emd_8753_validation.pdf.gz | 78.3 KB | Display | EMDB validaton report |
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Full document | emd_8753_full_validation.pdf.gz | 77.4 KB | Display | |
Data in XML | emd_8753_validation.xml.gz | 500 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8753 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8753 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8753.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-ET Tomogram of P. dulcis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 7.066 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Pandoravirus salinus
Entire | Name: Pandoravirus salinus |
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Components |
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-Supramolecule #1: Pandoravirus salinus
Supramolecule | Name: Pandoravirus salinus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1349410 / Sci species name: Pandoravirus salinus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Acanthamoeba (eukaryote) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Sugar embedding | Material: vitreous ice |
Grid | Model: Quantifoil 200 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV |
High pressure freezing | Instrument: OTHER Details: The value given for _emd_high_pressure_freezing.instrument is Leica EM PACT2. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION ...Details: The value given for _emd_high_pressure_freezing.instrument is Leica EM PACT2. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM HPM100', 'BAL-TEC HPM 010']) so OTHER is written into the XML file. |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Nanogold / Diameter: 10 nm |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD (ver. 4.7.15) / Number images used: 64 |
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