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- EMDB-15971: SARS-CoV-2 Delta-RBD complexed with Fabs BA.2-36, BA.2-23, EY6A a... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | SARS-CoV-2 Delta-RBD complexed with Fabs BA.2-36, BA.2-23, EY6A and COVOX-45 | |||||||||
![]() | CryoSPARC sharpened map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs. | |||||||||
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Function / homology | ![]() 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Duyvesteyn HME / Ren J / Stuart DI | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses. Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de ...Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de Silva / Megan Plowright / Thomas A H Newman / Hailey Hornsby / Alexander J Mentzer / Donal Skelly / Thomas G Ritter / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / / Cornelius Roemer / Thomas P Peacock / Neil G Paterson / Mark A Williams / David R Hall / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton / ![]() ![]() Abstract: In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or ...In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (mAbs) generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 230.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27 KB 27 KB | Display Display | ![]() |
Images | ![]() | 82.9 KB | ||
Others | ![]() ![]() | 225 MB 225 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bczMC ![]() 8bbnC ![]() 8bboC ![]() 8c3vC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | CryoSPARC sharpened map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.7303 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs.
File | emd_15971_half_map_1.map | ||||||||||||
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Annotation | Half map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs.
File | emd_15971_half_map_2.map | ||||||||||||
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Annotation | Half map of delta RBD BA2-23 BA2-36 EY6A and covox045 fabs. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Complex of SARS-CoV2 delta variant receptor binding domain with 4 Fabs
+Supramolecule #1: Complex of SARS-CoV2 delta variant receptor binding domain with 4 Fabs
+Supramolecule #2: SARS-CoV2 delta variant receptor binding domain
+Supramolecule #3: Antibody chains
+Macromolecule #1: Spike protein S1
+Macromolecule #2: BA.2-23 heavy chain
+Macromolecule #3: BA.2-23 light chain
+Macromolecule #4: COVOX-45 heavy chain
+Macromolecule #5: COVOX-45 light chain
+Macromolecule #6: EY6A heavy chain
+Macromolecule #7: EY6A light chain
+Macromolecule #8: BA.2-36 heavy chain
+Macromolecule #9: BA.2-36 light chain
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 35 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: Details: RBD, BA.2-23 and EY6A from PDB 7NX9, COVOX45 from pdb 7BEL, RBD and BA.2-36 Fab from 8BBO. |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 167492 |