ISDA

Entry Detail

PDB ID:

7YVM

EMDB ID:

EMD-34132

Keywords:

ANTIVIRAL PROTEIN/VIRAL PROTEIN

Title:

Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH272 Fab

Biological Source:

Source Organism:

Homo sapiens, Severe acute respiratory syndrome coronavirus 2

Host Organism:

Homo sapiens

PDB Version:

Deposition Date:

2022-08-19

Release Date:

2023-06-28

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.50 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Description:TH281 Fab light chain
Chain IDs:A
Chain Length:109
Number of Molecules:1
Biological Source:Homo sapiens

Protein Blast

Polymer Type:polypeptide(L)
Description:Spike glycoprotein
Mutations:K986P, V987P
Chain IDs:C (auth: B)
Chain Length:1288
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2

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

Polymer Type:polypeptide(L)
Description:TH281 Fab heavy chain
Chain IDs:B (auth: C)
Chain Length:118
Number of Molecules:1
Biological Source:Homo sapiens

Ligand Molecules

Primary Citation

Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection.

Guo, Y, Zhang, G, Yang, Q, Xie, X, Lu, Y, Cheng, X, Wang, H, Liang, J, Tang, J, Gao, Y, Shang, H, Dai, J, Shi, Y, Zhou, J, Zhou, J, Guo, H, Yang, H, Qi, J, Liu, L, Ma, S, Zhang, B, Huo, Q, Xie, Y, Wu, J, Dong, F, Zhang, S, Lou, Z, Gao, Y, Song, Z, Wang, W, Sun, Z, Yang, X, Xiong, D, Liu, F, Chen, X, Zhu, P, Wang, X, Cheng, T, Rao, Z.Show

Nat Commun 14 3537 3537 (2023)

PMID: 37322000 DOI: 10.1038/s41467-023-39267-x

Abstact

The SARS-CoV-2 Omicron variant evades most currently approved neutralizing antibodies (nAbs) and caused drastic decrease of plasma neutralizing activity elicited by vaccination or prior infection, urging the need for the development of pan-variant antivirals. Breakthrough infection induces a hybrid immunological response with potentially broad, potent and durable protection against variants, therefore, convalescent plasma from breakthrough infection may provide a broadened repertoire for identifying elite nAbs. We performed single-cell RNA sequencing (scRNA-seq) and BCR sequencing (scBCR-seq) of B cells from BA.1 breakthrough-infected patients who received 2 or 3 previous doses of inactivated vaccine. Elite nAbs, mainly derived from the IGHV2-5 and IGHV3-66/53 germlines, showed potent neutralizing activity across Wuhan-Hu-1, Delta, Omicron sublineages BA.1 and BA.2 at picomolar NT50 values. Cryo-EM analysis revealed diverse modes of spike recognition and guides the design of cocktail therapy. A single injection of paired antibodies cocktail provided potent protection in the K18-hACE2 transgenic female mouse model of SARS-CoV-2 infection.

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Primary Citation of related structures