[English] 日本語
Yorodumi- PDB-8gz6: Crystal structure of neutralizing VHH P17 in complex with SARS-Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gz6 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of neutralizing VHH P17 in complex with SARS-CoV-2 Alpha variant spike receptor-binding domain | ||||||||||||
Components | Nanobody P17 | ||||||||||||
Keywords | IMMUNE SYSTEM / SARS-CoV-2 / spike RBD / nanobody / VHH / VIRAL PROTEIN | ||||||||||||
Biological species | Vicugna pacos (alpaca) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||||||||
Authors | Yamaguchi, K. / Anzai, I. / Maeda, R. / Moriguchi, M. / Watanabe, T. / Imura, A. / Takaori-Kondo, A. / Inoue, T. | ||||||||||||
Funding support | Japan, 3items
| ||||||||||||
Citation | Journal: J.Biochem. / Year: 2023 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gz6.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gz6.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 8gz6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gz6_validation.pdf.gz | 435.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8gz6_full_validation.pdf.gz | 435.4 KB | Display | |
Data in XML | 8gz6_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 8gz6_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/8gz6 ftp://data.pdbj.org/pub/pdb/validation_reports/gz/8gz6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 13574.040 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|