ISDA

Entry Detail

PDB ID:

7TCC

EMDB ID:

EMD-25808

Keywords:

VIRAL PROTEIN/Immune System

Title:

Cryo-EM structure of SARS-CoV-2 Omicron spike in complex with antibodies A19-46.1 and B1-182.1

Biological Source:

Source Organism:

Severe acute respiratory syndrome coronavirus 2, Homo sapiens

Host Organism:

Homo sapiens

PDB Version:

Deposition Date:

2021-12-23

Release Date:

2022-03-30

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.86 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:Spike glycoprotein
Chain IDs:A, B, C
Chain Length:1272
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2

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

Polymer Type:polypeptide(L)
Description:Heavy chain of antibody A19-46.1
Chain IDs:D, H, J (auth: M)
Chain Length:126
Number of Molecules:3
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Description:Light chain of antibody A19-46.1
Chain IDs:E, I (auth: L), K (auth: N)
Chain Length:110
Number of Molecules:3
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Description:heavy chain of antibody B1-182.1
Chain IDs:F (auth: J), L (auth: O), N (auth: F)
Chain Length:123
Number of Molecules:3
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Description:Light chain of antibody B1-182.1
Chain IDs:G (auth: K), M (auth: P), O (auth: G)
Chain Length:108
Number of Molecules:3
Biological Source:Homo sapiens

Ligand Molecules

NAG

Primary Citation

Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529.

Zhou, T, Wang, L, Misasi, J, Pegu, A, Zhang, Y, Harris, D.R, Olia, A.S, Talana, C.A, Yang, E.S, Chen, M, Choe, M, Shi, W, Teng, I.T, Creanga, A, Jenkins, C, Leung, K, Liu, T, Stancofski, E.D, Stephens, T, Zhang, B, Tsybovsky, Y, Graham, B.S, Mascola, J.R, Sullivan, N.J, Kwong, P.D.Show

Science 376 eabn8897 eabn8897 (2022)

PMID: 35324257 DOI: 10.1126/science.abn8897

Abstact

The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (Omicron) variant and its resistance to neutralization by vaccinee and convalescent sera are driving a search for monoclonal antibodies with potent neutralization. To provide insight into effective neutralization, we determined cryo-electron microscopy structures and evaluated receptor binding domain (RBD) antibodies for their ability to bind and neutralize B.1.1.529. Mutations altered 16% of the B.1.1.529 RBD surface, clustered on an RBD ridge overlapping the angiotensin-converting enzyme 2 (ACE2)-binding surface and reduced binding of most antibodies. Substantial inhibitory activity was retained by select monoclonal antibodies-including A23-58.1, B1-182.1, COV2-2196, S2E12, A19-46.1, S309, and LY-CoV1404-that accommodated these changes and neutralized B.1.1.529. We identified combinations of antibodies with synergistic neutralization. The analysis revealed structural mechanisms for maintenance of potent neutralization against emerging variants.

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Chemical

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Primary Citation of related structures