7CHE | pdb_00007che

Crystal structure of the SARS-CoV-2 RBD in complex with BD-236 Fab and BD-368-2 Fab

• PDB DOI: https://doi.org/10.2210/pdb7CHE/pdb

• Classification: ANTIVIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens, Trichoplusia ni
• Mutation(s): No 


• Deposited: 2020-07-05 Released: 2020-09-16 
• Deposition Author(s): Xiao, J., Zhu, Q.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.42 Å
• R-Value Free: 
  0.239 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Structurally Resolved SARS-CoV-2 Antibody Shows High Efficacy in Severely Infected Hamsters and Provides a Potent Cocktail Pairing Strategy.

Du, S., Cao, Y., Zhu, Q., Yu, P., Qi, F., Wang, G., Du, X., Bao, L., Deng, W., Zhu, H., Liu, J., Nie, J., Zheng, Y., Liang, H., Liu, R., Gong, S., Xu, H., Yisimayi, A., Lv, Q., Wang, B., He, R., Han, Y., Zhao, W., Bai, Y., Qu, Y., Gao, X., Ji, C., Wang, Q., Gao, N., Huang, W., Wang, Y., Xie, X.S., Su, X.D., Xiao, J., Qin, C.

(2020) Cell 183: 1013-1023.e13

• PubMed: 32970990 
• DOI: https://doi.org/10.1016/j.cell.2020.09.035
• Primary Citation Related Structures: 
  7CH4, 7CH5, 7CHB, 7CHC, 7CHE, 7CHF, 7CHH


• PubMed 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; 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.

---

Organizational Affiliation: 
• School of Life Sciences, Peking University, Beijing 100871, China.
Beijing Advanced Innovation Center for Genomics (ICG) & Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China.
Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China.
School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG) & Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China.
Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China.
Beijing Advanced Innovation Center for Genomics (ICG) & Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China.
School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China.
School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG) & Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: [e-mail].
School of Life Sciences, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG) & Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China; State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China. Electronic address: [e-mail].
School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China. Electronic address: [e-mail].
Key Laboratory of Human Disease Comparative Medicine, Chinese Ministry of Health, Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 119.81 kDa 
• Atom Count: 7,956 
• Modeled Residue Count: 1,047 
• Deposited Residue Count: 1,109 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BD-236 Fab heavy chain	A [auth H]	223	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BD-236 Fab light chain	B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth R]	223	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BD-368-2 Fab heavy chain	D [auth A]	230	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
BD-368-2 Fab light chain	E [auth B]	219	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.42 Å
• R-Value Free:  0.239 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.016	α = 90
b = 114.296	β = 90
c = 116.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Xiao, J., Zhu, Q.

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2020-10-07
  Changes: Database references
• Version 1.2: 2020-11-25
  Changes: Database references
• Version 1.3: 2021-03-10
  Changes: Structure summary
• Version 1.4: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary