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Yorodumi- EMDB-32670: Cryo-EM structure of SARS-CoV-2 S2P trimer in complex with neutra... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32670 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209 | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.27 Å | |||||||||
Authors | Zheng Q / Sun H | |||||||||
Funding support | 1 items
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Citation | Journal: Cell Res / Year: 2022 Title: Immune escape by SARS-CoV-2 Omicron variant and structural basis of its effective neutralization by a broad neutralizing human antibody VacW-209. Authors: Bin Ju / Qingbing Zheng / Huimin Guo / Qing Fan / Tingting Li / Shuo Song / Hui Sun / Senlin Shen / Xinrong Zhou / Wenhui Xue / Lingyan Cui / Bing Zhou / Shaowei Li / Ningshao Xia / Zheng Zhang / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32670.map.gz | 685.1 MB | EMDB map data format | |
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Header (meta data) | emd-32670-v30.xml emd-32670.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | emd_32670.png | 31.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32670 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32670 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32670.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.778 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209
Entire | Name: SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209 |
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Components |
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-Supramolecule #1: SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209
Supramolecule | Name: SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209 type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #2: antibantibody VacW-209
Supramolecule | Name: antibantibody VacW-209 / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: SARS-CoV-2 S2P
Supramolecule | Name: SARS-CoV-2 S2P / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 320451 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |