ISDA

Deposition Date 2022-02-10

Release Date 2022-12-07

Last Version Date 2024-11-06

Entry Detail

PDB ID:

7WVL

Keywords:

VIRAL PROTEIN/IMMUNE SYSTEM

Title:

Structure of P4A2 Fab in complex with Spike-RBD from SARS-CoV-2

Biological Source:

Source Organism:

Mus musculus (Taxon ID: 10090)
Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.00 Å

R-Value Free:

0.27

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 31 2 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:C (auth: F)
Chain Length:223
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF09408

Polymer Type:polypeptide(L)
Molecule:P4A2 Fab heavy chain
Chain IDs:B (auth: H)
Chain Length:212
Number of Molecules:1
Biological Source:Mus musculus

Polymer Type:polypeptide(L)
Molecule:P4A2 Fab Light Chain
Chain IDs:A (auth: L)
Chain Length:218
Number of Molecules:1
Biological Source:Mus musculus

Primary Citation

A broadly neutralizing monoclonal antibody overcomes the mutational landscape of emerging SARS-CoV-2 variants of concern.

Parray, H.A, Narayanan, N, Garg, S, Rizvi, Z.A, Shrivastava, T, Kushwaha, S, Singh, J, Murugavelu, P, Anantharaj, A, Mehdi, F, Raj, N, Singh, S, Dandotiya, J, Lukose, A, Jamwal, D, Kumar, S, Chiranjivi, A, Dhyani, S, Mishra, N, Kumar, S, Jakhar, K, Sonar, S, Panchal, A.K, Tripathy, M.R, Chowdhury, S.R, Ahmed, S, Samal, S, Mani, S, Bhattacharyya, S, Das, S, Sinha, S, Luthra, K, Batra, G, Sehgal, D, Medigeshi, G.R, Sharma, C, Awasthi, A, Garg, P.K, Nair, D.T, Kumar, R.Show

Plos Pathog. 18 e1010994 e1010994 (2022)

PMID: 36508467 DOI: 10.1371/journal.ppat.1010994

Abstact

The emergence of new variants of SARS-CoV-2 necessitates unremitting efforts to discover novel therapeutic monoclonal antibodies (mAbs). Here, we report an extremely potent mAb named P4A2 that can neutralize all the circulating variants of concern (VOCs) with high efficiency, including the highly transmissible Omicron. The crystal structure of the P4A2 Fab:RBD complex revealed that the residues of the RBD that interact with P4A2 are a part of the ACE2-receptor-binding motif and are not mutated in any of the VOCs. The pan coronavirus pseudotyped neutralization assay confirmed that the P4A2 mAb is specific for SARS-CoV-2 and its VOCs. Passive administration of P4A2 to K18-hACE2 transgenic mice conferred protection, both prophylactically and therapeutically, against challenge with VOCs. Overall, our data shows that, the P4A2 mAb has immense therapeutic potential to neutralize the current circulating VOCs. Due to the overlap between the P4A2 epitope and ACE2 binding site on spike-RBD, P4A2 may also be highly effective against a number of future variants.

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