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Open data
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Basic information
Entry | Database: PDB / ID: 7f5g | |||||||||
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Title | The crystal structure of RBD-Nanobody complex, DL4 (SA4) | |||||||||
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![]() | VIRAL PROTEIN / Nanobody / RBD / neutralizing antibody / receptor-binding domain / SARS-CoV-2 | |||||||||
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 / entry receptor-mediated virion attachment to host cell ...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 / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Li, T. / Lai, Y. / Zhou, Y. / Tan, J. / Li, D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Isolation, characterization, and structure-based engineering of a neutralizing nanobody against SARS-CoV-2. Authors: Li, T. / Zhou, B. / Li, Y. / Huang, S. / Luo, Z. / Zhou, Y. / Lai, Y. / Gautam, A. / Bourgeau, S. / Wang, S. / Bao, J. / Tan, J. / Lavillette, D. / Li, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 200 KB | Display | ![]() |
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PDB format | ![]() | 127.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5m13S ![]() 6m0jS S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
-Protein / Antibody / Sugars , 3 types, 6 molecules ACBD
#1: Protein | Mass: 23747.643 Da / Num. of mol.: 2 / Fragment: Receptor binding domain (RBD) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() ![]() #2: Antibody | Mass: 16186.630 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Polysaccharide | Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 3 types, 639 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
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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: 2.83 Å3/Da / Density % sol: 60.89 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6 and 25% w/v Polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→36.58 Å / Num. obs: 91752 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 20 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.033 / Rrim(I) all: 0.117 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.183 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4455 / CC1/2: 0.898 / Rpim(I) all: 0.522 / Rrim(I) all: 1.288 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6M0J, 5M13 Resolution: 1.75→36.58 Å / SU ML: 0.1796 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2857 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: 29.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→36.58 Å
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Refine LS restraints |
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LS refinement shell |
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