6XC2

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.1

• PDB DOI:  https://doi.org/10.2210/pdb6XC2/pdb

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


• Deposited: 2020-06-08 Released: 2020-07-08 
• Deposition Author(s): Yuan, M., Liu, H., Wu, N.C., Zhu, X., Wilson, I.A.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation, Consortia for HIV/AIDS Vaccine Development

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.267 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Literature

Structural basis of a shared antibody response to SARS-CoV-2.

Yuan, M., Liu, H., Wu, N.C., Lee, C.D., Zhu, X., Zhao, F., Huang, D., Yu, W., Hua, Y., Tien, H., Rogers, T.F., Landais, E., Sok, D., Jardine, J.G., Burton, D.R., Wilson, I.A.

(2020) Science 369: 1119-1123

• PubMed: 32661058 
• DOI: https://doi.org/10.1126/science.abd2321
• Primary Citation of Related Structures:  
  6XC2, 6XC3, 6XC4, 6XC7


• PubMed Abstract: 
  

Molecular understanding of neutralizing antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could accelerate vaccine design and drug discovery. We analyzed 294 anti-SARS-CoV-2 antibodies and found that immunoglobulin G heavy-chain variable region 3-53 (IGHV3-53) is the most frequently used IGHV gene for targeting the receptor-binding domain (RBD) of the spike protein. Co-crystal structures of two IGHV3-53-neutralizing antibodies with RBD, with or without Fab CR3022, at 2.33- to 3.20-angstrom resolution revealed that the germline-encoded residues dominate recognition of the angiotensin I converting enzyme 2 (ACE2)-binding site. This binding mode limits the IGHV3-53 antibodies to short complementarity-determining region H3 loops but accommodates light-chain diversity. These IGHV3-53 antibodies show minimal affinity maturation and high potency, which is promising for vaccine design. Knowledge of these structural motifs and binding mode should facilitate the design of antigens that elicit this type of neutralizing response.

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Related Citations: 

• Structural basis of a public antibody response to SARS-CoV-2.
  Yuan, M., Liu, H., Wu, N.C., Lee, C.D., Zhu, X., Zhao, F., Huang, D., Yu, W., Hua, Y., Tien, H., Rogers, T.F., Landais, E., Sok, D., Jardine, J.G., Burton, D.R., Wilson, I.A.
  (2020) Biorxiv --: --

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Organizational Affiliation: 

The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 146.22 kDa 
• Atom Count: 9,584 
• Modelled Residue Count: 1,246 
• Deposited Residue Count: 1,336 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, D [auth Z]	231	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CC12.1 light chain	B [auth L], E [auth Y]	217	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CC12.1 heavy chain	C [auth H], F [auth X]	220	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth Z]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 0.267 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.699	α = 90
b = 143.494	β = 118.68
c = 81.469	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Yuan, M., Liu, H., Wu, N.C., Zhu, X., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI139445
Bill & Melinda Gates Foundation	United States	OPP1170236
Consortia for HIV/AIDS Vaccine Development	United States	UM1 AI44462

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2020-09-16
  Changes: Database references, Structure summary