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Open data
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Basic information
Entry | Database: PDB / ID: 7xb0 | ||||||
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Title | Crystal structure of Omicron BA.2 RBD complexed with hACE2 | ||||||
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![]() | HYDROLASE/VIRAL PROTEIN / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() positive regulation of amino acid transport / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, L. / Liao, H. / Meng, Y. / Li, W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of human ACE2 higher binding affinity to currently circulating Omicron SARS-CoV-2 sub-variants BA.2 and BA.1.1. Authors: Li, L. / Liao, H. / Meng, Y. / Li, W. / Han, P. / Liu, K. / Wang, Q. / Li, D. / Zhang, Y. / Wang, L. / Fan, Z. / Zhang, Y. / Wang, Q. / Zhao, X. / Sun, Y. / Huang, N. / Qi, J. / Gao, G.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 380.5 KB | Display | ![]() |
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PDB format | ![]() | 273.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7xazC ![]() 7xb1C ![]() 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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1 |
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | ![]() Mass: 69038.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: Mammalian expression vector EGFP-MCS-pcDNA3.1 (others) References: UniProt: Q9BYF1, ![]() ![]() |
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#2: Protein | Mass: 22039.873 Da / Num. of mol.: 1 / Fragment: Omicron BA.2 RBD Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2 Production host: Mammalian expression vector EGFP-MCS-pcDNA3.1 (others) References: UniProt: P0DTC2 |
-Sugars , 3 types, 6 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||
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#4: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #6: Sugar | ![]() |
-Non-polymers , 1 types, 1 molecules ![](data/chem/img/ZN.gif)
#5: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.29 Å3/Da / Density % sol: 62.62 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 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: 2.9→50 Å / Num. obs: 26827 / % possible obs: 96.5 % / Redundancy: 8.8 % / Biso Wilson estimate: 53.32 Å2 / CC1/2: 0.988 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.9→3 Å / Num. unique obs: 2649 / CC1/2: 0.727 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6LZG Resolution: 2.9→19.66 Å / SU ML: 0.284 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9446 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: 58.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.66 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 |
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