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Open data
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Basic information
Entry | Database: PDB / ID: 8suo | ||||||
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Title | BA.2/AZD1061/AZD3152 structure analysis | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / monoclonal antibody / broadly neutralizing / ACE-2 blocking / RBD binding / 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 / membrane fusion / Attachment and Entry / 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 | ![]() ![]() ![]() | ||||||
![]() | Oganesyan, V. / van Dyk, N. / Dippel, A. / Barnes, A. / O'Connor, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: X-ray crystal structure of BA.2 RBD bound by two neutralizing antibodies Authors: Oganesyan, V. / van Dyk, N. / Dippel, A. / Barnes, A. / O'Connor, E. / Riguero, V. / Taleb, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225 KB | Display | ![]() |
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PDB format | ![]() | 171.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.6 KB | Display | ![]() |
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Full document | ![]() | 467.6 KB | Display | |
Data in XML | ![]() | 37.9 KB | Display | |
Data in CIF | ![]() | 51.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l7eS ![]() 7ub0S ![]() 7zffS 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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Unit cell |
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Components
#1: Antibody | Mass: 24834.895 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Antibody | Mass: 24077.725 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Antibody | Mass: 24117.016 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Antibody | Mass: 22572.928 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 22039.873 Da / Num. of mol.: 1 / Fragment: receptor-binding domain (UNP residues 333-527) / Source method: isolated from a natural source Source: (natural) ![]() ![]() Variant: BA.2 / Strain: Omicron / References: UniProt: P0DTC2 |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.12 M D-glucose, 0.12 M D-mannose, 0.12 M D-galactose, 0.12 M L-fructose, 0.12 M D-xylose, 0.12 M N-acetyl-D-glucosamine, 0.1 M Tris, 0.1 M bicine, pH 8.5, 40% v/v ethylene glycol, 20% w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX325HE / Detector: CCD / Date: Sep 23, 2022 |
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→94.36 Å / Num. obs: 36925 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.98→3.06 Å / Num. unique obs: 2697 / CC1/2: 0.275 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries 7L7E, 7UB0, & 7ZFF Resolution: 3.3→30.002 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.842 / WRfactor Rfree: 0.332 / WRfactor Rwork: 0.279 / SU B: 46.281 / SU ML: 0.682 / Average fsc free: 0.8809 / Average fsc work: 0.9126 / Cross valid method: THROUGHOUT / ESU R Free: 0.627 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 120.958 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→30.002 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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