7MMO | pdb_00007mmo

LY-CoV1404 neutralizing antibody against SARS-CoV-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.253 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.226 (Depositor) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants.

Westendorf, K.Wang, L.Zentelis, S.Foster, D.Vaillancourt, P.Wiggin, M.Lovett, E.van der Lee, R.Hendle, J.Pustilnik, A.Sauder, J.M.Kraft, L.Hwang, Y.Siegel, R.W.Chen, J.Heinz, B.A.Higgs, R.E.Kallewaard, N.Jepson, K.Goya, R.Smith, M.A.Collins, D.W.Pellacani, D.Xiang, P.de Puyraimond, V.Ricicova, M.Devorkin, L.Pritchard, C.O'Neill, A.Dalal, K.Panwar, P.Dhupar, H.Garces, F.A.Cohen, C.Dye, J.Huie, K.E.Badger, C.V.Kobasa, D.Audet, J.Freitas, J.J.Hassanali, S.Hughes, I.Munoz, L.Palma, H.C.Ramamurthy, B.Cross, R.W.Geisbert, T.W.Menacherry, V.Lokugamage, K.Borisevich, V.Lanz, I.Anderson, L.Sipahimalani, P.Corbett, K.S.Yang, E.S.Zhang, Y.Shi, W.Zhou, T.Choe, M.Misasi, J.Kwong, P.D.Sullivan, N.J.Graham, B.S.Fernandez, T.L.Hansen, C.L.Falconer, E.Mascola, J.R.Jones, B.E.Barnhart, B.C.

(2022) bioRxiv 

  • DOI: https://doi.org/10.1101/2021.04.30.442182
  • Primary Citation Related Structures: 
    7MMO

  • PubMed Abstract: 

    SARS-CoV-2 neutralizing monoclonal antibodies (mAbs) can reduce the risk of hospitalization when administered early during COVID-19 disease. However, the emergence of variants of concern has negatively impacted the therapeutic use of some authorized mAbs. Using a high throughput B-cell screening pipeline, we isolated a highly potent SARS-CoV-2 spike glycoprotein receptor binding domain (RBD)-specific antibody called LY-CoV1404 (also known as bebtelovimab). LY-CoV1404 potently neutralizes authentic SARS-CoV-2 virus, including the prototype, B.1.1.7, B.1.351 and B.1.617.2). In pseudovirus neutralization studies, LY-CoV1404 retains potent neutralizing activity against numerous variants including B.1.1.7, B.1.351, B.1.617.2, B.1.427/B.1.429, P.1, B.1.526, B.1.1.529, and the BA.2 subvariant and retains binding to spike proteins with a variety of underlying RBD mutations including K417N, L452R, E484K, and N501Y. Structural analysis reveals that the contact residues of the LY-CoV1404 epitope are highly conserved with the exception of N439 and N501. Notably, the binding and neutralizing activity of LY-CoV1404 is unaffected by the most common mutations at these positions (N439K and N501Y). The breadth of reactivity to amino acid substitutions present among current VOC together with broad and potent neutralizing activity and the relatively conserved epitope suggest that LY-CoV1404 has the potential to be an effective therapeutic agent to treat all known variants causing COVID-19. LY-CoV1404 is a potent SARS-CoV-2-binding antibody that neutralizes all known variants of concern and whose epitope is rarely mutated. LY-CoV1404 potently neutralizes SARS-CoV-2 authentic virus and known variants of concern including the B.1.1.529 (Omicron), the BA.2 Omicron subvariant, and B.1.617.2 (Delta) variantsNo loss of potency against currently circulating variantsBinding epitope on RBD of SARS-CoV-2 is rarely mutated in GISAID databaseBreadth of neutralizing activity and potency supports clinical development.

Macromolecule Content 

  • Total Structure Weight: 140.79 kDa 
  • Atom Count: 9,153 
  • Modeled Residue Count: 1,217 
  • Deposited Residue Count: 1,286 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LY-CoV1404 Fab heavy chain
A, D
223Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LY-CoV1404 Fab light chain
B, E
215Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S1
C, F
205Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A, D
L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.253 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.226 (Depositor) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.094α = 90
b = 107.692β = 90
c = 190.472γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references
  • Version 1.2: 2022-01-26
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary