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- PDB-8gz6: Crystal structure of neutralizing VHH P17 in complex with SARS-Co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gz6 | ||||||||||||
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Title | Crystal structure of neutralizing VHH P17 in complex with SARS-CoV-2 Alpha variant spike receptor-binding domain | ||||||||||||
![]() | Nanobody P17 | ||||||||||||
![]() | IMMUNE SYSTEM / SARS-CoV-2 / spike RBD / nanobody / VHH / VIRAL PROTEIN | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Yamaguchi, K. / Anzai, I. / Maeda, R. / Moriguchi, M. / Watanabe, T. / Imura, A. / Takaori-Kondo, A. / Inoue, T. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the rational design of a nanobody that binds with high affinity to the SARS-CoV-2 spike variant. Authors: Yamaguchi, K. / Anzai, I. / Maeda, R. / Moriguchi, M. / Watanabe, T. / Imura, A. / Takaori-Kondo, A. / Inoue, T. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.9 KB | Display | ![]() |
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PDB format | ![]() | 87.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 13574.040 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris propane pH 8.5, 24.5% w/v polyethylene glycol 6000 |
-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: Apr 17, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→42.18 Å / Num. obs: 46794 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.32 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.042 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.35→1.37 Å / Num. unique obs: 2408 / CC1/2: 0.686 / Rrim(I) all: 0.885 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8GZ5 Resolution: 1.35→42.18 Å / SU ML: 0.1776 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.1923 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→42.18 Å
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Refine LS restraints |
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LS refinement shell |
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