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- EMDB-33047: Cryo-EM structure of SARS-CoV-2 spike protein in complex with thr... -
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Basic information
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Title | Cryo-EM structure of SARS-CoV-2 spike protein in complex with three nAbs X01, X10 and X17 | |||||||||
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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 / 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
![]() | Sun H / Liu L / Zheng Q / Li S / Zhang T / Xia N | |||||||||
Funding support | 1 items
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![]() | ![]() Title: The neutralizing breadth of antibodies targeting diverse conserved epitopes between SARS-CoV and SARS-CoV-2. Authors: Hualong Xiong / Hui Sun / Siling Wang / Lunzhi Yuan / Liqin Liu / Yuhe Zhu / Jinlei Zhang / Yang Huang / Ruoyao Qi / Yao Jiang / Jian Ma / Ming Zhou / Yue Ma / Rao Fu / Siping Yan / Mingxi ...Authors: Hualong Xiong / Hui Sun / Siling Wang / Lunzhi Yuan / Liqin Liu / Yuhe Zhu / Jinlei Zhang / Yang Huang / Ruoyao Qi / Yao Jiang / Jian Ma / Ming Zhou / Yue Ma / Rao Fu / Siping Yan / Mingxi Yue / Yangtao Wu / Min Wei / Yizhen Wang / Tingting Li / Yingbin Wang / Zizheng Zheng / Hai Yu / Tong Cheng / Shaowei Li / Quan Yuan / Jun Zhang / Yi Guan / Qingbing Zheng / Tianying Zhang / Ningshao Xia / ![]() Abstract: Antibody therapeutics for the treatment of COVID-19 have been highly successful. However, the recent emergence of the Omicron variant has posed a challenge, as it evades detection by most existing ...Antibody therapeutics for the treatment of COVID-19 have been highly successful. However, the recent emergence of the Omicron variant has posed a challenge, as it evades detection by most existing SARS-CoV-2 neutralizing antibodies (nAbs). Here, we successfully generated a panel of SARS-CoV-2/SARS-CoV cross-neutralizing antibodies by sequential immunization of the two pseudoviruses. Of the potential candidates, we found that nAbs X01, X10, and X17 offer broad neutralizing potential against most variants of concern, with X17 further identified as a Class 5 nAb with undiminished neutralization against the Omicron variant. Cryo-electron microscopy structures of the three antibodies together in complex with each of the spike proteins of the prototypical SARS-CoV, SARS-CoV-2, and Delta and Omicron variants of SARS-CoV-2 defined three nonoverlapping conserved epitopes on the receptor-binding domain. The triple-antibody mixture exhibited enhanced resistance to viral evasion and effective protection against infection of the Beta variant in hamsters. Our findings will aid the development of antibody therapeutics and broad vaccines against SARS-CoV-2 and its emerging variants. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 229.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18 KB 18 KB | Display Display | ![]() |
Images | ![]() | 47.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 400.8 KB | Display | ![]() |
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Full document | ![]() | 400.3 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Data in CIF | ![]() | 8.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7x7tMC ![]() 7x7uC ![]() 7x7vC 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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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.778 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Cryo-EM structure of SARS-CoV-2 spike protein in complex with thr...
+Supramolecule #1: Cryo-EM structure of SARS-CoV-2 spike protein in complex with thr...
+Supramolecule #2: SARS-CoV-2 spike protein
+Supramolecule #3: nAbs X01, X10 and X17
+Macromolecule #1: Spike protein S1
+Macromolecule #2: X10 light chain
+Macromolecule #3: X10 heavy chain
+Macromolecule #4: X17 light chain
+Macromolecule #5: X17 heavy chain
+Macromolecule #6: X01 light chain
+Macromolecule #7: X01 heavy chain
+Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1028337 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |