+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39113 | |||||||||
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Title | SARS-CoV-2 DMV nsp3-4 pore complex (mini-pore) | |||||||||
Map data | local resolution map | |||||||||
Sample |
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Keywords | Double membrane vesicle / pore complex / nsp3 / nsp4 / RNA transport / VIRAL PROTEIN | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Huang YX / Zhong LJ / Zhang WX / Ni T | |||||||||
Funding support | Hong Kong, 1 items
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Citation | Journal: To Be Published Title: Molecular Architecture of Coronavirus Double Membrane Vesicle Pore Complex Authors: Huang YX / Ni T #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018 Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Afonine PV / Adams PD | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39113.map.gz | 51.6 MB | EMDB map data format | |
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Header (meta data) | emd-39113-v30.xml emd-39113.xml | 16 KB 16 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_39113_fsc.xml | 10.2 KB | Display | FSC data file |
Images | emd_39113.png | 101.4 KB | ||
Masks | emd_39113_msk_1.map | 91.1 MB | Mask map | |
Filedesc metadata | emd-39113.cif.gz | 4.8 KB | ||
Others | emd_39113_half_map_1.map.gz emd_39113_half_map_2.map.gz | 43.5 MB 43.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39113 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39113 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_39113.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | local resolution map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.571 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_39113_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_39113_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_39113_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SARS-CoV-2 DMV nsp3-4 pore complex
Entire | Name: SARS-CoV-2 DMV nsp3-4 pore complex |
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Components |
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-Supramolecule #1: SARS-CoV-2 DMV nsp3-4 pore complex
Supramolecule | Name: SARS-CoV-2 DMV nsp3-4 pore complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
Details: 150mM NaCl, 10mM Tris-HCl, 1mM EDTA | ||||||||||||
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Grid | Model: EMS Lacey Carbon / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 3.0 e/Å2 Details: The tilt-series were acquired using Thermofisher Krios equipped with a Falcon 4i camera and Selectris energy filter. A dose-symmetric scheme (group of 2) was used, with a tilt range of -51 ...Details: The tilt-series were acquired using Thermofisher Krios equipped with a Falcon 4i camera and Selectris energy filter. A dose-symmetric scheme (group of 2) was used, with a tilt range of -51 to 51 (or -60 to 60) at 3 degree increments and an exposure dose of 3 e-/A2 per image. The total dose was 105 (or 123) e-/A2. |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT |