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- PDB-7ch5: Crystal structure of the SARS-CoV-2 S RBD in complex with BD-629 Fab -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ch5 | ||||||
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Title | Crystal structure of the SARS-CoV-2 S RBD in complex with BD-629 Fab | ||||||
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![]() | PROTEIN BINDING/IMMUNE SYSTEM / Complex / PROTEIN BINDING-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 / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / 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 | ![]() ![]() ![]() | ||||||
![]() | Du, S. / Xiao, J.Y. | ||||||
![]() | ![]() Title: Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy. Authors: Shuo Du / Yunlong Cao / Qinyu Zhu / Pin Yu / Feifei Qi / Guopeng Wang / Xiaoxia Du / Linlin Bao / Wei Deng / Hua Zhu / Jiangning Liu / Jianhui Nie / Yinghui Zheng / Haoyu Liang / Ruixue Liu ...Authors: Shuo Du / Yunlong Cao / Qinyu Zhu / Pin Yu / Feifei Qi / Guopeng Wang / Xiaoxia Du / Linlin Bao / Wei Deng / Hua Zhu / Jiangning Liu / Jianhui Nie / Yinghui Zheng / Haoyu Liang / Ruixue Liu / Shuran Gong / Hua Xu / Ayijiang Yisimayi / Qi Lv / Bo Wang / Runsheng He / Yunlin Han / Wenjie Zhao / Yali Bai / Yajin Qu / Xiang Gao / Chenggong Ji / Qisheng Wang / Ning Gao / Weijin Huang / Youchun Wang / X Sunney Xie / Xiao-Dong Su / Junyu Xiao / Chuan Qin / ![]() Abstract: Understanding how potent neutralizing antibodies (NAbs) inhibit SARS-CoV-2 is critical for effective therapeutic development. We previously described BD-368-2, a SARS-CoV-2 NAb with high potency; ...Understanding how potent neutralizing antibodies (NAbs) inhibit SARS-CoV-2 is critical for effective therapeutic development. We previously described BD-368-2, a SARS-CoV-2 NAb with high potency; however, its neutralization mechanism is largely unknown. Here, we report the 3.5-Å cryo-EM structure of BD-368-2/trimeric-spike complex, revealing that BD-368-2 fully blocks ACE2 recognition by occupying all three receptor-binding domains (RBDs) simultaneously, regardless of their "up" or "down" conformations. Also, BD-368-2 treats infected adult hamsters at low dosages and at various administering windows, in contrast to placebo hamsters that manifested severe interstitial pneumonia. Moreover, BD-368-2's epitope completely avoids the common binding site of VH3-53/VH3-66 recurrent NAbs, evidenced by tripartite co-crystal structures with RBDs. Pairing BD-368-2 with a potent recurrent NAb neutralizes SARS-CoV-2 pseudovirus at pM level and rescues mutation-induced neutralization escapes. Together, our results rationalized a new RBD epitope that leads to high neutralization potency and demonstrated BD-368-2's therapeutic potential in treating COVID-19. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.4 KB | Display | ![]() |
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PDB format | ![]() | 100.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7ch4C ![]() 7chbC ![]() 7chcC ![]() 7cheC ![]() 7chfC ![]() 7chhC ![]() 6m0jS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 23774.537 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 23273.830 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 25122.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Production host: ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.44 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0 and 18% w/v Polyethylene glycol 20000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 26831 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.993 / Net I/σ(I): 13.78 |
Reflection shell | Resolution: 2.7→2.75 Å / Num. unique obs: 1283 / CC1/2: 0.906 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6M0J Resolution: 2.7→49.16 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.5 / 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: 99.7 Å2 / Biso mean: 44.8019 Å2 / Biso min: 20.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→49.16 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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