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- PDB-7wsk: Crystal structure of SARS-CoV-2 Omicron spike receptor-binding do... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wsk | ||||||
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Title | Crystal structure of SARS-CoV-2 Omicron spike receptor-binding domain in complex with civet ACE2 | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, B. / Han, P. / Qi, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Broader-species receptor binding and structural bases of Omicron SARS-CoV-2 to both mouse and palm-civet ACE2s. Authors: Linjie Li / Pu Han / Baihan Huang / Yufeng Xie / Weiwei Li / Di Zhang / Pengcheng Han / Zepeng Xu / Bin Bai / Jingya Zhou / Xinrui Kang / Xiaomei Li / Anqi Zheng / Rong Zhang / Shitong Qiao ...Authors: Linjie Li / Pu Han / Baihan Huang / Yufeng Xie / Weiwei Li / Di Zhang / Pengcheng Han / Zepeng Xu / Bin Bai / Jingya Zhou / Xinrui Kang / Xiaomei Li / Anqi Zheng / Rong Zhang / Shitong Qiao / Xin Zhao / Jianxun Qi / Qihui Wang / Kefang Liu / George Fu Gao / ![]() Abstract: The Omicron variant of SARS-CoV-2 carries multiple unusual mutations, particularly in the receptor-binding domain (RBD) of the spike (S) protein. Moreover, host-adapting mutations, such as residues ...The Omicron variant of SARS-CoV-2 carries multiple unusual mutations, particularly in the receptor-binding domain (RBD) of the spike (S) protein. Moreover, host-adapting mutations, such as residues 493, 498, and 501, were also observed in the Omicron RBD, which indicates that it is necessary to evaluate the interspecies transmission risk of the Omicron variant. Herein, we evaluated the interspecies recognition of the Omicron BA.1 and Delta RBDs by 27 ACE2 orthologs, including humans. We found that Omicron BA.1 expanded its receptor binding spectra to palm-civet, rodents, more bats (least horseshoe bat and greater horseshoe bat) and lesser hedgehog tenrec. Additionally, we determined the cryo-electron microscopy (cryo-EM) structure of the Omicron BA.1 S protein complexed with mouse ACE2 (mACE2) and the crystal structure of Omicron RBD complexed with palm-civet ACE2 (cvACE2). Several key residues for the host range have been identified. These results suggest that surveillance should be enhanced on the Omicron variant for its broader-species receptor binding to prevent spillover and expansion of reservoir hosts for a prolonged pandemic. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 380.9 KB | Display | ![]() |
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PDB format | ![]() | 275.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7wrhC ![]() 7wriC ![]() 6lzgS S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 69529.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 25415.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2 / Cell line (production host): HEK293 / Production host: ![]() ![]() | ||||
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-3)-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 / ![]() #5: Chemical | ChemComp-ZN / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.89 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Potassium thiocyanate, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.3→50 Å / Num. obs: 19998 / % possible obs: 99.7 % / Redundancy: 11.4 % / Biso Wilson estimate: 68.79 Å2 / Rmerge(I) obs: 0.453 / Rsym value: 0.453 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 3.3→3.42 Å / Rmerge(I) obs: 1.549 / Num. unique obs: 1951 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6LZG Resolution: 3.3→20.66 Å / SU ML: 0.4338 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3063 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→20.66 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1
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