+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23889 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Prefusion-stabilized SARS-CoV-2 VFLIP_D614G spike | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.88 Å | |||||||||
Authors | Olmedillas E / Ollmann Saphire E / Diaz Avalos R | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: To Be Published Title: Prefusion-stabilized SARS-CoV-2 VFLIP_D614G spike Authors: Olmedillas E / Ollmann Saphire E / Diaz Avalos R | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_23889.map.gz | 229.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-23889-v30.xml emd-23889.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_23889.png | 67.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23889 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23889 | HTTPS FTP |
-Validation report
Summary document | emd_23889_validation.pdf.gz | 336.7 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_23889_full_validation.pdf.gz | 336.3 KB | Display | |
Data in XML | emd_23889_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_23889_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23889 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23889 | HTTPS FTP |
-Related structure data
Related structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_23889.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.66 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : Prefusion-stabilized SARS-CoV-2 VFLIP variant D614G spike glycoprotein
Entire | Name: Prefusion-stabilized SARS-CoV-2 VFLIP variant D614G spike glycoprotein |
---|---|
Components |
|
-Supramolecule #1: Prefusion-stabilized SARS-CoV-2 VFLIP variant D614G spike glycoprotein
Supramolecule | Name: Prefusion-stabilized SARS-CoV-2 VFLIP variant D614G spike glycoprotein type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Molecular weight | Theoretical: 660 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| |||||||||
Grid | Model: C-flat | |||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Min: 83.0 K / Max: 110.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 2 / Number real images: 3000 / Average exposure time: 1.5 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
---|