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Open data
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Basic information
Entry | Database: PDB / ID: 7f6z | ||||||
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Title | Complex Structure of antibody BD-503 and RBD-501Y.V2 of COVID-19 | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / COVID-19 / SARS-CoV-2 / Neutralization Antibody / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
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 / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, H. / Wang, B. / Zhao, T.N. / Su, X.D. | ||||||
![]() | ![]() Title: Structure-based analyses of neutralization antibodies interacting with naturally occurring SARS-CoV-2 RBD variants. Authors: Xu, H. / Wang, B. / Zhao, T.N. / Liang, Z.T. / Peng, T.B. / Song, X.H. / Wu, J.J. / Wang, Y.C. / Su, X.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 | ![]() | 250.7 KB | Display | ![]() |
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PDB format | ![]() | 199.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 763.1 KB | Display | ![]() |
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Full document | ![]() | 768.5 KB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ejyC ![]() 7ejzC ![]() 7ek0C ![]() 7f6ySC S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components
#1: Protein | Mass: 25156.398 Da / Num. of mol.: 1 / Fragment: receptor binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
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#2: Antibody | Mass: 23215.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Antibody | Mass: 23415.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium sulfate, 0.1M Tris, pH 8.5, 12% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3→19.994 Å / Num. obs: 36180 / % possible obs: 99.45 % / Redundancy: 6.1 % / Biso Wilson estimate: 68.18 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.09 / Rrim(I) all: 0.22 / Net I/σ(I): 8.33 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1777 / CC1/2: 0.9 / Rpim(I) all: 0.43 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7F6Y Resolution: 3→19.994 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 27.57 / 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: 118.3 Å2 / Biso mean: 61.8142 Å2 / Biso min: 38.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→19.994 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -2.2993 Å / Origin y: -39.6486 Å / Origin z: -4.9406 Å
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Refinement TLS group |
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