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- PDB-7urq: Crystal Structure of SARS-CoV-2 S delta variant receptor-binding ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7urq | ||||||||||||
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Title | Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex CoV11 Fab crystal form 1 | ||||||||||||
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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 | ![]() ![]() ![]() | ||||||||||||
![]() | Tolbert, W.D. / Pazgier, M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The molecular basis of the neutralization breadth of the RBD-specific antibody CoV11. Authors: Tolbert, W.D. / Chen, Y. / Sun, L. / Benlarbi, M. / Ding, S. / Manickam, R. / Pangaro, E. / Nguyen, D.N. / Gottumukkala, S. / Cote, M. / Gonzalez, F.J. / Finzi, A. / Tehrani, Z.R. / Sajadi, M.M. / Pazgier, 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 | ![]() | 265.6 KB | Display | ![]() |
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PDB format | ![]() | 210.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7s4sSC ![]() 7ursC 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
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 23362.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#3: Antibody | Mass: 23536.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 25946.182 Da / Num. of mol.: 1 / Mutation: L452R, T478K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: S, 2 / Cell (production host): HEK 293 GnT1- / Production host: ![]() ![]() |
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#4: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 2 types, 244 molecules ![](data/chem/img/CIT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CIT / ![]() |
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#6: Water | ChemComp-HOH / ![]() |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.02 % |
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Crystal grow![]() | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10% PEG 4000 0.2 M sodium acetate 0.1 M sodium citrate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2022 |
Radiation | Monochromator: Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.05→50 Å / Num. obs: 59785 / % possible obs: 93.3 % / Redundancy: 5.6 % / CC1/2: 0.986 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.056 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2350 / CC1/2: 0.485 / Rpim(I) all: 0.467 / % possible all: 74.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7S4S Resolution: 2.05→41.23 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.85 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→41.23 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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