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- PDB-7jvb: Crystal structure of the SARS-CoV-2 spike receptor-binding domain... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jvb | ||||||
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Title | Crystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with nanobody Nb20 | ||||||
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Function / homology | ![]() Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xiang, Y. / Xiao, Z. / Liu, H. / Sang, Z. / Schneidman-Duhovny, D. / Zhang, C. / Shi, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2. Authors: Xiang, Y. / Nambulli, S. / Xiao, Z. / Liu, H. / Sang, Z. / Duprex, W.P. / Schneidman-Duhovny, D. / Zhang, C. / Shi, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 257.8 KB | Display | ![]() |
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PDB format | ![]() | 208.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6waqS S: Starting model for refinement |
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Similar 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: Protein | Mass: 25179.389 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2 / Production host: ![]() ![]() ![]() #2: Antibody | Mass: 12553.048 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-CAC / ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.87 % |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM sodium cacodylate pH 6.5, 1 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.287→38.96 Å / Num. obs: 17442 / % possible obs: 96.34 % / Redundancy: 6.2 % / Biso Wilson estimate: 98.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.108 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3.287→3.405 Å / Rmerge(I) obs: 0.591 / Num. unique obs: 1391 / CC1/2: 0.811 / Rpim(I) all: 0.445 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6WAQ Resolution: 3.287→38.959 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.287→38.959 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -16.1778 Å / Origin y: -15.3348 Å / Origin z: -27.1171 Å
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Refinement TLS group | Selection details: all |