+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35239 | |||||||||
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Title | Prefusion spike of BA.1 with all-RBD-down conformation | |||||||||
Map data | Subtomgram-averaged density map of BA.1 prefusion spike with all-RBD-down conformation | |||||||||
Sample |
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Keywords | Cryo-ET / Subtomogram averaging / Omicron / prefusion spike / VIRAL PROTEIN | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 8.3 Å | |||||||||
Authors | Gao YZ / Ma XY / Liu Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Prefusion Spike Protein of SARS-CoV-2 sublineage BA.1.1 in RBD down conformation Authors: Gao YZ / Ma XY / Liu Z | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35239.map.gz | 3.2 MB | EMDB map data format | |
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Header (meta data) | emd-35239-v30.xml emd-35239.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35239_fsc.xml | 3.5 KB | Display | FSC data file |
Images | emd_35239.png | 29.6 KB | ||
Filedesc metadata | emd-35239.cif.gz | 3.7 KB | ||
Others | emd_35239_half_map_1.map.gz emd_35239_half_map_2.map.gz | 2.4 MB 2.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35239 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35239 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35239.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Subtomgram-averaged density map of BA.1 prefusion spike with all-RBD-down conformation | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.66 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Subtomgram-averaged density map of BA.1 prefusion spike with...
File | emd_35239_half_map_1.map | ||||||||||||
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Annotation | Subtomgram-averaged density map of BA.1 prefusion spike with all-RBD-down conformation, half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Subtomgram-averaged density map of BA.1 prefusion spike with...
File | emd_35239_half_map_2.map | ||||||||||||
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Annotation | Subtomgram-averaged density map of BA.1 prefusion spike with all-RBD-down conformation, half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Severe acute respiratory syndrome coronavirus 2
Entire | Name: Severe acute respiratory syndrome coronavirus 2 |
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Components |
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-Supramolecule #1: Severe acute respiratory syndrome coronavirus 2
Supramolecule | Name: Severe acute respiratory syndrome coronavirus 2 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: BA.1.1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN 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 / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.92 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |