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- PDB-8h5t: Crystal structure of SARS-CoV-2 spike receptor-binding domain in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h5t | ||||||
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Title | Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-015 | ||||||
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![]() | VIRAL PROTEIN / IMMUNE SYSTEM | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Yang, J. / Lin, S. / Lu, G.W. | ||||||
Funding support | 1items
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![]() | ![]() Title: Development of a bispecific nanobody conjugate broadly neutralizes diverse SARS-CoV-2 variants and structural basis for its broad neutralization. Authors: Yang, J. / Lin, S. / Chen, Z. / Yang, F. / Guo, L. / Wang, L. / Duan, Y. / Zhang, X. / Dai, Y. / Yin, K. / Yu, C. / Yuan, X. / Sun, H. / He, B. / Cao, Y. / Ye, H. / Dong, H. / Liu, X. / ...Authors: Yang, J. / Lin, S. / Chen, Z. / Yang, F. / Guo, L. / Wang, L. / Duan, Y. / Zhang, X. / Dai, Y. / Yin, K. / Yu, C. / Yuan, X. / Sun, H. / He, B. / Cao, Y. / Ye, H. / Dong, H. / Liu, X. / Chen, B. / Li, J. / Zhao, Q. / Lu, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.9 KB | Display | ![]() |
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PDB format | ![]() | 106.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8h5uC ![]() 5tp3S ![]() 6yz5S 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: 24501.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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#2: Antibody | Mass: 14281.753 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium formate, pH 7.2, 20% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 22938 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 46.136 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.664 / Num. unique obs: 2299 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6YZ5, 5TP3 Resolution: 2→26.152 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.09 / 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: 94.56 Å2 / Biso mean: 45.28 Å2 / Biso min: 22.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→26.152 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -2.9867 Å / Origin y: 15.2311 Å / Origin z: -0.6199 Å
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Refinement TLS group |
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