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Open data
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Basic information
Entry | Database: PDB / ID: 7ejz | ||||||
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Title | Complex Structure of antibody BD-503 and RBD-S477N 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 / 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 / symbiont-mediated suppression of host innate immune response / 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 / identical protein binding / membrane / 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 | ![]() | 252.2 KB | Display | ![]() |
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PDB format | ![]() | 201.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ejyC ![]() 7ek0C ![]() 7f6yC ![]() 7f6zC ![]() 7bwjS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 25149.359 Da / Num. of mol.: 1 / Fragment: Receptor binding domain / Mutation: S477N 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: Sugar | ChemComp-NAG / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.14 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M Magnesium chloride hexahydrate, 0.1M Sodium citrate, pH 5.0, 15% (w/v) PEG 4000 |
-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: Jan 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.63→41.66 Å / Num. obs: 10003 / % possible obs: 95.96 % / Redundancy: 12.8 % / Biso Wilson estimate: 62.33 Å2 / CC1/2: 0.958 / CC star: 0.989 / Rpim(I) all: 0.1301 / Rrim(I) all: 0.4691 / Net I/σ(I): 7.96 |
Reflection shell | Resolution: 3.633→3.763 Å / Redundancy: 12.9 % / Num. unique obs: 930 / CC1/2: 0.862 / CC star: 0.962 / Rpim(I) all: 0.2923 / % possible all: 81.45 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7BWJ Resolution: 3.63→41.66 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.31 / 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: 189.65 Å2 / Biso mean: 71.8559 Å2 / Biso min: 36.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.63→41.66 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Origin x: -2.4828 Å / Origin y: 39.3908 Å / Origin z: 4.9858 Å
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Refinement TLS group |
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