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Yorodumi- EMDB-33204: S-ECD (Omicron) in complex with PD of ACE2 focused on RBD_PD sub-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33204 | |||||||||
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Title | S-ECD (Omicron) in complex with PD of ACE2 focused on RBD_PD sub-complex | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Li YN / Shen YP / Zhang YY / Yan RH | |||||||||
Funding support | China, 1 items
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Citation | Journal: iScience / Year: 2022 Title: Structural and functional analysis of an inter-Spike bivalent neutralizing antibody against SARS-CoV-2 variants. Authors: Yaning Li / Qing Fan / Bing Zhou / Yaping Shen / Yuanyuan Zhang / Lin Cheng / Furong Qi / Shuo Song / Yingying Guo / Renhong Yan / Bin Ju / Zheng Zhang / Abstract: The different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have attracted most public concern because they caused "wave and wave" COVID-19 pandemic. The initial step of ...The different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have attracted most public concern because they caused "wave and wave" COVID-19 pandemic. The initial step of viral infection is mediated by the SARS-CoV-2 Spike (S) protein, which mediates the receptor recognition and membrane fusion between virus and host cells. Neutralizing antibodies (nAbs) targeting the S protein of SARS-CoV-2 have become promising candidates for clinical intervention strategy, while multiple studies have shown that different variants have enhanced infectivity and antibody resistance. Here, we explore the structure and function of STS165, a broadly inter-Spike bivalent nAb against SARS-CoV-2 variants and even SARS-CoV, contributing to further understanding of the working mechanism of nAbs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33204.map.gz | 86 MB | EMDB map data format | |
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Header (meta data) | emd-33204-v30.xml emd-33204.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_33204.png | 19.9 KB | ||
Others | emd_33204_half_map_1.map.gz emd_33204_half_map_2.map.gz | 84.5 MB 84.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33204 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33204 | HTTPS FTP |
-Validation report
Summary document | emd_33204_validation.pdf.gz | 774.6 KB | Display | EMDB validaton report |
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Full document | emd_33204_full_validation.pdf.gz | 774.2 KB | Display | |
Data in XML | emd_33204_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_33204_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33204 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33204 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33204.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33204_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33204_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : S-ECD (Omicron) in complex with PD of ACE2
Entire | Name: S-ECD (Omicron) in complex with PD of ACE2 |
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Components |
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-Supramolecule #1: S-ECD (Omicron) in complex with PD of ACE2
Supramolecule | Name: S-ECD (Omicron) in complex with PD of ACE2 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #2: S-ECD (Omicron)
Supramolecule | Name: S-ECD (Omicron) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: ACE2
Supramolecule | Name: ACE2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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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: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 2.2 µm / Nominal defocus min: 1.2 µm |
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
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 65532 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |