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Yorodumi- EMDB-32944: The complex structure of Omicron BA.1 RBD with BD604, S309,and S304 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32944 | |||||||||
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Title | The complex structure of Omicron BA.1 RBD with BD604, S309,and S304 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | antibody viral protein complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.74 Å | |||||||||
Authors | Huang M / Xie YF | |||||||||
Funding support | China, 1 items
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Citation | Journal: Immunity / Year: 2022 Title: Atlas of currently available human neutralizing antibodies against SARS-CoV-2 and escape by Omicron sub-variants BA.1/BA.1.1/BA.2/BA.3. Authors: Min Huang / Lili Wu / Anqi Zheng / Yufeng Xie / Qingwen He / Xiaoyu Rong / Pu Han / Pei Du / Pengcheng Han / Zengyuan Zhang / Runchu Zhao / Yunfei Jia / Linjie Li / Bin Bai / Ziliang Hu / ...Authors: Min Huang / Lili Wu / Anqi Zheng / Yufeng Xie / Qingwen He / Xiaoyu Rong / Pu Han / Pei Du / Pengcheng Han / Zengyuan Zhang / Runchu Zhao / Yunfei Jia / Linjie Li / Bin Bai / Ziliang Hu / Shixiong Hu / Sheng Niu / Yu Hu / Honghui Liu / Bo Liu / Kaige Cui / Weiwei Li / Xin Zhao / Kefang Liu / Jianxun Qi / Qihui Wang / George Fu Gao / Abstract: SARS-CoV-2 Omicron variant has presented significant challenges to current antibodies and vaccines. Herein, we systematically compared the efficacy of 50 human monoclonal antibodies (mAbs), covering ...SARS-CoV-2 Omicron variant has presented significant challenges to current antibodies and vaccines. Herein, we systematically compared the efficacy of 50 human monoclonal antibodies (mAbs), covering the seven identified epitope classes of the SARS-CoV-2 RBD, against Omicron sub-variants BA.1, BA.1.1, BA.2, and BA.3. Binding and pseudovirus-based neutralizing assays revealed that 37 of the 50 mAbs lost neutralizing activities, whereas the others displayed variably decreased activities against the four Omicron sub-variants. BA.2 was found to be more sensitive to RBD-5 antibodies than the other sub-variants. Furthermore, a quaternary complex structure of BA.1 RBD with three mAbs showing different neutralizing potencies against Omicron provided a basis for understanding the immune evasion of Omicron sub-variants and revealed the lack of G446S mutation accounting for the sensitivity of BA.2 to RBD-5 mAbs. Our results may guide the application of the available mAbs and facilitate the development of universal therapeutic antibodies and vaccines against COVID-19. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32944.map.gz | 167.9 MB | EMDB map data format | |
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Header (meta data) | emd-32944-v30.xml emd-32944.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32944_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_32944.png | 53.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32944 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32944 | HTTPS FTP |
-Validation report
Summary document | emd_32944_validation.pdf.gz | 578.1 KB | Display | EMDB validaton report |
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Full document | emd_32944_full_validation.pdf.gz | 577.6 KB | Display | |
Data in XML | emd_32944_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_32944_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32944 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32944 | HTTPS FTP |
-Related structure data
Related structure data | 7x1mMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32944.map.gz / Format: CCP4 / Size: 178 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: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : BD604 Fab, S309 Fab and S304 Fab complex with Omicron BA.1 RBD
+Supramolecule #1: BD604 Fab, S309 Fab and S304 Fab complex with Omicron BA.1 RBD
+Supramolecule #2: BD604 Fab, S309 Fab and S304 Fab
+Supramolecule #3: Omicron BA.1 RBD
+Macromolecule #1: S309 Fab heavy chain
+Macromolecule #2: S309 Fab light chain
+Macromolecule #3: BD-604 Fab heavy chain
+Macromolecule #4: BD-604 Fab light chain
+Macromolecule #5: S304 Fab haavy chain
+Macromolecule #6: S304 Fab light chain
+Macromolecule #7: Spike protein S1
-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 (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: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |