7L3N | pdb_00007l3n

SARS-CoV 2 Spike Protein bound to LY-CoV555


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7L3N

This is version 1.1 of the entry. See complete history

Literature

LY-CoV555, a rapidly isolated potent neutralizing antibody, provides protection in a non-human primate model of SARS-CoV-2 infection.

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.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.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.

(2020) bioRxiv 

  • DOI: https://doi.org/10.1101/2020.09.30.318972
  • Primary Citation Related Structures: 
    7L3N

  • PubMed Abstract: 

    SARS-CoV-2 poses a public health threat for which therapeutic agents are urgently needed. Herein, we report that high-throughput microfluidic screening of antigen-specific B-cells led to the identification of LY-CoV555, a potent anti-spike neutralizing antibody from a convalescent COVID-19 patient. Biochemical, structural, and functional characterization revealed high-affinity binding to the receptor-binding domain, ACE2 binding inhibition, and potent neutralizing activity. In a rhesus macaque challenge model, prophylaxis doses as low as 2.5 mg/kg reduced viral replication in the upper and lower respiratory tract. These data demonstrate that high-throughput screening can lead to the identification of a potent antiviral antibody that protects against SARS-CoV-2 infection. LY-CoV555, an anti-spike antibody derived from a convalescent COVID-19 patient, potently neutralizes SARS-CoV-2 and protects the upper and lower airways of non-human primates against SARS-CoV-2 infection.

Macromolecule Content 

  • Total Structure Weight: 475.78 kDa 
  • Atom Count: 24,118 
  • Modeled Residue Count: 3,056 
  • Deposited Residue Count: 4,268 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,276Severe 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: 6Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
LY-CoV555 Fab heavy chain228Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
LY-CoV555 Fab light chain212Homo sapiensMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

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

Query on NAG



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.27 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary