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- PDB-6xc4: Crystal structure of SARS-CoV-2 receptor binding domain in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xc4 | ||||||||||||
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Title | Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.3 | ||||||||||||
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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 | ![]() ![]() ![]() | ||||||||||||
![]() | Yuan, M. / Liu, H. / Wu, N.C. / Zhu, X. / Wilson, I.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of a shared antibody response to SARS-CoV-2. Authors: Yuan, M. / Liu, H. / Wu, N.C. / Lee, C.D. / Zhu, X. / Zhao, F. / Huang, D. / Yu, W. / Hua, Y. / Tien, H. / Rogers, T.F. / Landais, E. / Sok, D. / Jardine, J.G. / Burton, D.R. / Wilson, I.A. #1: Journal: Biorxiv / Year: 2020 Title: Structural basis of a public antibody response to SARS-CoV-2. Authors: Yuan, M. / Liu, H. / Wu, N.C. / Lee, C.D. / Zhu, X. / Zhao, F. / Huang, D. / Yu, W. / Hua, Y. / Tien, H. / Rogers, T.F. / Landais, E. / Sok, D. / Jardine, J.G. / Burton, D.R. / Wilson, I.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 269.9 KB | Display | ![]() |
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PDB format | ![]() | 211.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6xc2C ![]() 6xc3C ![]() 6xc7C ![]() 4tsaS ![]() 4zd3S ![]() 6ylaS C: citing same article ( 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 26095.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2 / Production host: ![]() ![]() #2: Antibody | Mass: 23377.150 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Antibody | Mass: 23431.963 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Sugar | ![]() #5: 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: 3.36 Å3/Da / Density % sol: 63.45 % |
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Crystal grow![]() | Temperature: 298.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium phosphate pH 6.5 12% polyethylene glycol 8000 |
-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: May 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.33→50 Å / Num. obs: 78783 / % possible obs: 98.7 % / Redundancy: 2.4 % / CC1/2: 0.987 / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.33→2.38 Å / Rmerge(I) obs: 0.95 / Num. unique obs: 7298 / CC1/2: 0.51 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6YLA, 4TSA, 4ZD3 Resolution: 2.341→41.706 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.45 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 176.79 Å2 / Biso mean: 39.1926 Å2 / Biso min: 14.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.341→41.706 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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