6XKP

Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-270

• PDB DOI:  https://doi.org/10.2210/pdb6XKP/pdb

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


• Deposited: 2020-06-26 Released: 2020-10-14 
• Deposition Author(s): Liu, H., Yuan, M., Zhu, X., Wu, N.C., Wilson, I.A.
• Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.269 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 

Literature

A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model.

Kreye, J., Reincke, S.M., Kornau, H.C., Sanchez-Sendin, E., Corman, V.M., Liu, H., Yuan, M., Wu, N.C., Zhu, X., Lee, C.D., Trimpert, J., Holtje, M., Dietert, K., Stoffler, L., von Wardenburg, N., van Hoof, S., Homeyer, M.A., Hoffmann, J., Abdelgawad, A., Gruber, A.D., Bertzbach, L.D., Vladimirova, D., Li, L.Y., Barthel, P.C., Skriner, K., Hocke, A.C., Hippenstiel, S., Witzenrath, M., Suttorp, N., Kurth, F., Franke, C., Endres, M., Schmitz, D., Jeworowski, L.M., Richter, A., Schmidt, M.L., Schwarz, T., Muller, M.A., Drosten, C., Wendisch, D., Sander, L.E., Osterrieder, N., Wilson, I.A., Pruss, H.

(2020) Cell 183: 1058

• PubMed: 33058755 
• DOI: https://doi.org/10.1016/j.cell.2020.09.049
• Primary Citation of Related Structures:  
  6XKP, 6XKQ


• PubMed Abstract: 
  

The emergence of SARS-CoV-2 led to pandemic spread of coronavirus disease 2019 (COVID-19), manifesting with respiratory symptoms and multi-organ dysfunction. Detailed characterization of virus-neutralizing antibodies and target epitopes is needed to understand COVID-19 pathophysiology and guide immunization strategies. Among 598 human monoclonal antibodies (mAbs) from 10 COVID-19 patients, we identified 40 strongly neutralizing mAbs. The most potent mAb, CV07-209, neutralized authentic SARS-CoV-2 with an IC ₅₀ value of 3.1 ng/mL. Crystal structures of two mAbs in complex with the SARS-CoV-2 receptor-binding domain at 2.55 and 2.70 Å revealed a direct block of ACE2 attachment. Interestingly, some of the near-germline SARS-CoV-2-neutralizing mAbs reacted with mammalian self-antigens. Prophylactic and therapeutic application of CV07-209 protected hamsters from SARS-CoV-2 infection, weight loss, and lung pathology. Our results show that non-self-reactive virus-neutralizing mAbs elicited during SARS-CoV-2 infection are a promising therapeutic strategy.

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Organizational Affiliation: 

German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 148.46 kDa 
• Atom Count: 9,251 
• Modelled Residue Count: 1,253 
• Deposited Residue Count: 1,358 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A, B	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
CV07-270 Heavy Chain	C [auth H], E [auth M]	232	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CV07-270 Light Chain	D [auth L], F [auth N]	216	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	I [auth H], J [auth H], K [auth H], L, M [auth L], N [auth M], O [auth M], P [auth N]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.269 
• R-Value Work: 0.220 
• R-Value Observed: 0.222 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.02	α = 90
b = 151.785	β = 95.44
c = 66.015	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Liu, H., Yuan, M., Zhu, X., Wu, N.C., Wilson, I.A.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1170236
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI139445

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2020-11-04
  Changes: Database references
• Version 1.2: 2020-11-25
  Changes: Database references