8HN6

Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD

• PDB DOI: https://doi.org/10.2210/pdb8HN6/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli, Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2022-12-07 Released: 2023-05-17 
• Deposition Author(s): Qi, J., Chen, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.214 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents.

Wang, Z., Li, D., Chen, Y., Sun, Y., Jin, C., Hu, C., Feng, Y., Su, J., Ren, L., Hao, Y., Wang, S., Zhu, M., Liu, Y., Qi, J., Zhu, B., Shao, Y.

(2023) Front Immunol 14: 1160283-1160283

• PubMed: 37234155 
• DOI: https://doi.org/10.3389/fimmu.2023.1160283
• Primary Citation of Related Structures:  
  8HN6, 8HN7


• PubMed Abstract: 
  

  The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been posing a severe threat to global public health. Although broadly neutralizing antibodies have been used to prevent or treat corona virus disease 2019 (COVID-19), new emerging variants have been proven resistant to these antibodies.

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Organizational Affiliation: 

State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 6-mer - A4B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 92.74 kDa 
• Atom Count: 7,012 
• Modelled Residue Count: 839 
• Deposited Residue Count: 840 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of monoclonal antibody 3G10	A, D [auth C]	117	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of monoclonal antibody 3G10	B, E [auth D]	108	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C [auth E], F	195	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.214 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.68	α = 90
b = 105.73	β = 90
c = 209.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Qi, J., Chen, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2023-05-24
  Changes: Database references, Structure summary
• Version 1.2: 2023-06-07
  Changes: Database references