+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16767 | ||||||||||||||||||
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Title | In situ STA of rotavirus enveloped DLP (penton) | ||||||||||||||||||
Map data | consensus average | ||||||||||||||||||
Sample |
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Biological species | Rotavirus A | ||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 10.2 Å | ||||||||||||||||||
Authors | Shah PNM / Stuart DI | ||||||||||||||||||
Funding support | United Kingdom, 5 items
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Citation | Journal: Cell Host Microbe / Year: 2023 Title: Characterization of the rotavirus assembly pathway in situ using cryoelectron tomography Authors: Shah PN / Gilchrist JB / Forsberg BO / Burt A / Howe A / Mosalaganti S / Wan W / Radecke J / Chaban Y / Sutton G / Stuart DI / Boyce M | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16767.map.gz | 33 MB | EMDB map data format | |
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Header (meta data) | emd-16767-v30.xml emd-16767.xml | 14.7 KB 14.7 KB | Display Display | EMDB header |
Images | emd_16767.png | 182 KB | ||
Others | emd_16767_half_map_1.map.gz emd_16767_half_map_2.map.gz | 17.7 MB 17.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16767 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16767 | HTTPS FTP |
-Validation report
Summary document | emd_16767_validation.pdf.gz | 966.5 KB | Display | EMDB validaton report |
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Full document | emd_16767_full_validation.pdf.gz | 966.1 KB | Display | |
Data in XML | emd_16767_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | emd_16767_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16767 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16767 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16767.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | consensus average | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.97 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half1
File | emd_16767_half_map_1.map | ||||||||||||
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Annotation | half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half2
File | emd_16767_half_map_2.map | ||||||||||||
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Annotation | half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Rotavirus A
Entire | Name: Rotavirus A |
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Components |
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-Supramolecule #1: Rotavirus A
Supramolecule | Name: Rotavirus A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 28875 / Sci species name: Rotavirus A / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 1.0.9) / Number subtomograms used: 138 |
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Extraction | Number tomograms: 85 / Number images used: 138 / Software - Name: crYOLO (ver. 1.8.2) |
Final 3D classification | Software - Name: RELION (ver. 3.1.2) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.2) |