ISDA

Deposition Date 2022-03-28

Release Date 2022-10-12

Last Version Date 2025-07-02

Entry Detail

PDB ID:

7ZCE

Keywords:

VIRAL PROTEIN

Title:

SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)
Enterobacteria phage T4 (Taxon ID: 10665)
Homo sapiens (Taxon ID: 9606)

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.50 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein,Fibritin
Gene (Uniprot):S, wac
Chain IDs:A, B, C
Chain Length:1288
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2, Enterobacteria phage T4

UniProt ID:P0DTC2,P10104 Pfam ID:PF16451, PF09408, PF19209, PF01601

Polymer Type:polypeptide(L)
Molecule:scFv76 single chain fragment
Chain IDs:D (auth: E), E (auth: F), F (auth: G)
Chain Length:264
Number of Molecules:3
Biological Source:Homo sapiens

Ligand Molecules

NAG

Primary Citation

Spike mutation resilient scFv76 antibody counteracts SARS-CoV-2 lung damage upon aerosol delivery.

Milazzo, F.M, Chaves-Sanjuan, A, Minenkova, O, Santapaola, D, Anastasi, A.M, Battistuzzi, G, Chiapparino, C, Rosi, A, Merlo Pich, E, Albertoni, C, Marra, E, Luberto, L, Viollet, C, Spagnoli, L.G, Riccio, A, Rossi, A, Santoro, M.G, Ballabio, F, Paissoni, C, Camilloni, C, Bolognesi, M, De Santis, R.Show

Mol.Ther. 31 362 373 (2022)

PMID: 36114671 DOI: 10.1016/j.ymthe.2022.09.010

Abstact

The uneven worldwide vaccination coverage against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and emergence of variants escaping immunity call for broadly effective and easily deployable therapeutic agents. We have previously described the human single-chain scFv76 antibody, which recognizes SARS-CoV-2 Alpha, Beta, Gamma and Delta variants. We now show that scFv76 also neutralizes the infectivity and fusogenic activity of the Omicron BA.1 and BA.2 variants. Cryoelectron microscopy (cryo-EM) analysis reveals that scFv76 binds to a well-conserved SARS-CoV-2 spike epitope, providing the structural basis for its broad-spectrum activity. We demonstrate that nebulized scFv76 has therapeutic efficacy in a severe hACE2 transgenic mouse model of coronavirus disease 2019 (COVID-19) pneumonia, as shown by body weight and pulmonary viral load data. Counteraction of infection correlates with inhibition of lung inflammation, as observed by histopathology and expression of inflammatory cytokines and chemokines. Biomarkers of pulmonary endothelial damage were also significantly reduced in scFv76-treated mice. The results support use of nebulized scFv76 for COVID-19 induced by any SARS-CoV-2 variants that have emerged so far.

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