Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 71.63 kDa 
• Atom Count: 4820 
• Modelled Residue Count: 636 
• Deposited Residue Count: 662 
• Unique protein chains: 3

7BWJ

crystal structure of SARS-CoV-2 antibody with RBD

• DOI: 10.2210/pdb7BWJ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Spodoptera frugiperda, Homo sapiens
• Mutation(s): No 


• Deposited: 2020-04-14 Released: 2020-06-03 
• Deposition Author(s): Wang, X., Ge, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.264 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Literature

Human neutralizing antibodies elicited by SARS-CoV-2 infection.

Ju, B., Zhang, Q., Ge, J., Wang, R., Sun, J., Ge, X., Yu, J., Shan, S., Zhou, B., Song, S., Tang, X., Yu, J., Lan, J., Yuan, J., Wang, H., Zhao, J., Zhang, S., Wang, Y., Shi, X., Liu, L., Zhao, J., Wang, X., Zhang, Z., Zhang, L.

(2020) Nature 584: 115-119

• PubMed: 32454513 
• DOI: 10.1038/s41586-020-2380-z
• Primary Citation of Related Structures:  
  7BWJ


• PubMed Abstract: 
  

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents a global health emergency that is in urgent need of intervention ^1-3 . The entry of SARS-CoV-2 into its target cells depends on binding between the receptor-binding domain (RBD) of the viral spike protein and its cellular receptor, angiotensin-converting enzyme 2 (ACE2) ^2,4-6 . Here we report the isolation and characterization of 206 RBD-specific monoclonal antibodies derived from single B cells from 8 individuals infected with SARS-CoV-2. We identified antibodies that potently neutralize SARS-CoV-2; this activity correlates with competition with ACE2 for binding to RBD. Unexpectedly, the anti-SARS-CoV-2 antibodies and the infected plasma did not cross-react with the RBDs of SARS-CoV or Middle East respiratory syndrome-related coronavirus (MERS-CoV), although there was substantial plasma cross-reactivity to their trimeric spike proteins. Analysis of the crystal structure of RBD-bound antibody revealed that steric hindrance inhibits viral engagement with ACE2, thereby blocking viral entry. These findings suggest that anti-RBD antibodies are largely viral-species-specific inhibitors. The antibodies identified here may be candidates for development of clinical interventions against SARS-CoV-2.

---

Organizational Affiliation: 

Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center and Beijing Advanced Innovation Center for Structural Biology, School of Medicine, and Vanke School of Public Health, Tsinghua University, Beijing, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	E	217	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody light chain	L	216	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody heavy chain	H	229	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.264 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.23	α = 90
b = 90.15	β = 90
c = 112.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2020-04-14 
• Released Date: 2020-06-03 
Deposition Author(s): Wang, X., Ge, J.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2020-06-10
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2020-08-19
  Changes: Database references, Structure summary
• Version 1.4: 2021-03-10
  Changes: Structure summary