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- PDB-7ws8: Structures of Omicron Spike complexes illuminate broad-spectrum n... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ws8 | ||||||
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Title | Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development | ||||||
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Function / homology | ![]() positive regulation of amino acid transport / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guo, H. / Gao, Y. / Ji, X. / Yang, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of Omicron spike complexes and implications for neutralizing antibody development. Authors: Hangtian Guo / Yan Gao / Tinghan Li / Tingting Li / Yuchi Lu / Le Zheng / Yue Liu / Tingting Yang / Feiyang Luo / Shuyi Song / Wei Wang / Xiuna Yang / Henry C Nguyen / Hongkai Zhang / Ailong ...Authors: Hangtian Guo / Yan Gao / Tinghan Li / Tingting Li / Yuchi Lu / Le Zheng / Yue Liu / Tingting Yang / Feiyang Luo / Shuyi Song / Wei Wang / Xiuna Yang / Henry C Nguyen / Hongkai Zhang / Ailong Huang / Aishun Jin / Haitao Yang / Zihe Rao / Xiaoyun Ji / ![]() ![]() Abstract: The emergence of the SARS-CoV-2 Omicron variant is dominant in many countries worldwide. The high number of spike mutations is responsible for the broad immune evasion from existing vaccines and ...The emergence of the SARS-CoV-2 Omicron variant is dominant in many countries worldwide. The high number of spike mutations is responsible for the broad immune evasion from existing vaccines and antibody drugs. To understand this, we first present the cryo-electron microscopy structure of ACE2-bound SARS-CoV-2 Omicron spike. Comparison to previous spike antibody structures explains how Omicron escapes these therapeutics. Secondly, we report structures of Omicron, Delta, and wild-type spikes bound to a patient-derived Fab antibody fragment (510A5), which provides direct evidence where antibody binding is greatly attenuated by the Omicron mutations, freeing spike to bind ACE2. Together with biochemical binding and 510A5 neutralization assays, our work establishes principles of binding required for neutralization and clearly illustrates how the mutations lead to antibody evasion yet retain strong ACE2 interactions. Structural information on spike with both bound and unbound antibodies collectively elucidates potential strategies for generation of therapeutic antibodies. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 763 KB | Display | ![]() |
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PDB format | ![]() | 638.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 32750MC ![]() 7ws0C ![]() 7ws1C ![]() 7ws2C ![]() 7ws3C ![]() 7ws4C ![]() 7ws5C ![]() 7ws6C ![]() 7ws7C ![]() 7ws9C ![]() 7wsaC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | ![]() Mass: 133940.031 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2 / Production host: ![]() ![]() #2: Protein | Mass: 68967.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ![]() Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||||||
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118216 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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