7KMH | pdb_00007kmh

LY-CoV488 neutralizing antibody against SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb7KMH/pdb

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


• Deposited: 2020-11-02 Released: 2021-01-27 
• Deposition Author(s): Hendle, J., Pustilnik, A., Sauder, J.M., Boyles, J.S., Dickinson, C.D., Coleman, K.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates.

Jones, B.E., Brown-Augsburger, P.L., Corbett, K.S., Westendorf, K., Davies, J., Cujec, T.P., Wiethoff, C.M., Blackbourne, J.L., Heinz, B.A., Foster, D., Higgs, R.E., Balasubramaniam, D., Wang, L., Zhang, Y., Yang, E.S., Bidshahri, R., Kraft, L., Hwang, Y., Zentelis, S., Jepson, K.R., Goya, R., Smith, M.A., Collins, D.W., Hinshaw, S.J., Tycho, S.A., Pellacani, D., Xiang, P., Muthuraman, K., Sobhanifar, S., Piper, M.H., Triana, F.J., Hendle, J., Pustilnik, A., Adams, A.C., Berens, S.J., Baric, R.S., Martinez, D.R., Cross, R.W., Geisbert, T.W., Borisevich, V., Abiona, O., Belli, H.M., de Vries, M., Mohamed, A., Dittmann, M., Samanovic, M.I., Mulligan, M.J., Goldsmith, J.A., Hsieh, C.L., Johnson, N.V., Wrapp, D., McLellan, J.S., Barnhart, B.C., Graham, B.S., Mascola, J.R., Hansen, C.L., Falconer, E.

(2021) Sci Transl Med 13

• PubMed: 33820835 
• DOI: https://doi.org/10.1126/scitranslmed.abf1906
• Primary Citation Related Structures: 
  7KMG, 7KMH, 7KMI


• PubMed Abstract: 
  

  Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) poses a public health threat for which preventive and therapeutic agents are urgently needed. Neutralizing antibodies are a key class of therapeutics that may bridge widespread vaccination campaigns and offer a treatment solution in populations less responsive to vaccination. Here, we report that high-throughput microfluidic screening of antigen-specific B cells led to the identification of LY-CoV555 (also known as bamlanivimab), a potent anti-spike neutralizing antibody from a hospitalized, convalescent patient with coronavirus disease 2019 (COVID-19). Biochemical, structural, and functional characterization of LY-CoV555 revealed high-affinity binding to the receptor-binding domain, angiotensin-converting enzyme 2 binding inhibition, and potent neutralizing activity. A pharmacokinetic study of LY-CoV555 conducted in cynomolgus monkeys demonstrated a mean half-life of 13 days and a clearance of 0.22 ml hour ^-1 kg ^-1 , consistent with a typical human therapeutic antibody. In a rhesus macaque challenge model, prophylactic doses as low as 2.5 mg/kg reduced viral replication in the upper and lower respiratory tract in samples collected through study day 6 after viral inoculation. This antibody has entered clinical testing and is being evaluated across a spectrum of COVID-19 indications, including prevention and treatment.

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Organizational Affiliation: 
• Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA. [e-mail] [e-mail].
Eli Lilly and Company, Indianapolis, IN 46225, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
AbCellera Biologics Inc., Vancouver, BC V5Y0A1, Canada.
Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA.
University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Galveston National Laboratory and Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
Department of Population Health, Division of Biostatistics, New York University Grossman School of Medicine, New York, NY 10016, USA.
Department of Microbiology, New York University Grossman School of Medicine, New York, NY 10016, USA.
NYU Langone Vaccine Center, Department of Medicine, Division of Infectious Diseases and Immunology, New York University Grossman School of Medicine, New York, NY 10016, USA.
Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
AbCellera Biologics Inc., Vancouver, BC V5Y0A1, Canada. [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.19 kDa 
• Atom Count: 4,923 
• Modeled Residue Count: 616 
• Deposited Residue Count: 636 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LY-CoV488 Fab heavy chain	A	219	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LY-CoV488 Fab light chain	B	212	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	C	205	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PRO	F [auth C]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
GOL	E [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.806	α = 90
b = 260.59	β = 90
c = 94.997	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Hendle, J., Pustilnik, A., Sauder, J.M., Boyles, J.S., Dickinson, C.D., Coleman, K.A.

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2021-09-01
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary