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Yorodumi- EMDB-33894: Omicron Spike trimer bound with side P3E6 Fab (1 RBD up and 2 RBD... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33894 | |||||||||
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Title | Omicron Spike trimer bound with side P3E6 Fab (1 RBD up and 2 RBDs down) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | COVID-19 / P3E6 / Omicron / spike protein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.27 Å | |||||||||
Authors | Tang B / Dang S | |||||||||
Funding support | Hong Kong, 1 items
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Citation | Journal: Emerg Microbes Infect / Year: 2023 Title: Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2. Authors: Mengxiao Luo / Biao Zhou / Eswar R Reddem / Bingjie Tang / Bohao Chen / Runhong Zhou / Hang Liu / Lihong Liu / Phinikoula S Katsamba / Ka-Kit Au / Hiu-On Man / Kelvin Kai-Wang To / Kwok-Yung ...Authors: Mengxiao Luo / Biao Zhou / Eswar R Reddem / Bingjie Tang / Bohao Chen / Runhong Zhou / Hang Liu / Lihong Liu / Phinikoula S Katsamba / Ka-Kit Au / Hiu-On Man / Kelvin Kai-Wang To / Kwok-Yung Yuen / Lawrence Shapiro / Shangyu Dang / David D Ho / Zhiwei Chen / Abstract: Increasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth ...Increasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth and structural insights of bNAbs derived from memory B cells of BNT162b2-vaccinee after homogeneous Omicron BA.1 breakthrough infection. The infection activates diverse memory B cell clonotypes for generating potent class I/II and III bNAbs with new epitopes mapped to the receptor-binding domain (RBD). The top eight bNAbs neutralize wildtype and BA.1 potently but display divergent IgH/IgL sequences and neuralization profiles against other variants of concern (VOCs). Two of them (P2D9 and P3E6) belonging to class III NAbs display comparable potency against BA.4/BA.5, although structural analysis reveals distinct modes of action. P3E6 neutralizes all variants tested through a unique bivalent interaction with two RBDs. Our findings provide new insights into hybrid immunity on BNT162b2-induced diverse memory B cells in response to Omicron breakthrough infection for generating diverse bNAbs with distinct structural basis. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33894.map.gz | 62.4 MB | EMDB map data format | |
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Header (meta data) | emd-33894-v30.xml emd-33894.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_33894.png | 38.3 KB | ||
Filedesc metadata | emd-33894.cif.gz | 4 KB | ||
Others | emd_33894_half_map_1.map.gz emd_33894_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33894 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33894 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33894.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33894_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33894_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The complex of Omicron Spike trimer bound with P3E6 Fab
Entire | Name: The complex of Omicron Spike trimer bound with P3E6 Fab |
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Components |
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-Supramolecule #1: The complex of Omicron Spike trimer bound with P3E6 Fab
Supramolecule | Name: The complex of Omicron Spike trimer bound with P3E6 Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
-Supramolecule #2: Spike glycoprotein
Supramolecule | Name: Spike glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: P3E6 Fab
Supramolecule | Name: P3E6 Fab / 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: 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82194 |