+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33579 | |||||||||
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Title | map focused on the interface between BA.2 RBD and ACE2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SARS-Cov-2 / VIRAL PROTEIN / VIRAL PROTEIN-HYDROLASE complex | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Li YN / Shen YP / Zhang YY / Yan RH | |||||||||
Funding support | China, 1 items
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Citation | Journal: Viruses / Year: 2023 Title: Structural Basis for the Enhanced Infectivity and Immune Evasion of Omicron Subvariants. Authors: Yaning Li / Yaping Shen / Yuanyuan Zhang / Renhong Yan / Abstract: The Omicron variants of SARS-CoV-2 have emerged as the dominant strains worldwide, causing the COVID-19 pandemic. Each Omicron subvariant contains at least 30 mutations on the spike protein (S ...The Omicron variants of SARS-CoV-2 have emerged as the dominant strains worldwide, causing the COVID-19 pandemic. Each Omicron subvariant contains at least 30 mutations on the spike protein (S protein) compared to the original wild-type (WT) strain. Here we report the cryo-EM structures of the trimeric S proteins from the BA.1, BA.2, BA.3, and BA.4/BA.5 subvariants, with BA.4 and BA.5 sharing the same S protein mutations, each in complex with the surface receptor ACE2. All three receptor-binding domains of the S protein from BA.2 and BA.4/BA.5 are "up", while the BA.1 S protein has two "up" and one "down". The BA.3 S protein displays increased heterogeneity, with the majority in the all "up" RBD state. The different conformations preferences of the S protein are consistent with their varied transmissibility. By analyzing the position of the glycan modification on Asn343, which is located at the S309 epitopes, we have uncovered the underlying immune evasion mechanism of the Omicron subvariants. Our findings provide a molecular basis of high infectivity and immune evasion of Omicron subvariants, thereby offering insights into potential therapeutic interventions against SARS-CoV-2 variants. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33579.map.gz | 86 MB | EMDB map data format | |
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Header (meta data) | emd-33579-v30.xml emd-33579.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_33579.png | 19.9 KB | ||
Others | emd_33579_half_map_1.map.gz emd_33579_half_map_2.map.gz | 84.6 MB 84.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33579 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33579 | HTTPS FTP |
-Validation report
Summary document | emd_33579_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_33579_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_33579_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_33579_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33579 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33579 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33579.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_33579_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33579_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : S-ECD (Omicron BA.3) in complex with 2 PD of ACE2
Entire | Name: S-ECD (Omicron BA.3) in complex with 2 PD of ACE2 |
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Components |
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-Supramolecule #1: S-ECD (Omicron BA.3) in complex with 2 PD of ACE2
Supramolecule | Name: S-ECD (Omicron BA.3) in complex with 2 PD of ACE2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #2: S-ECD (Omicron BA.3)
Supramolecule | Name: S-ECD (Omicron BA.3) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: PD of ACE2
Supramolecule | Name: PD of ACE2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4 |
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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 |
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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
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 35756 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |