ISDA: 7YAD

Deposition Date 2022-06-27

Release Date 2022-08-31

Last Version Date 2024-11-13

Entry Detail

PDB ID:

7YAD

Keywords:

IMMUNE SYSTEM/VIRAL PROTEIN

Title:

Cryo-EM structure of S309-RBD-RBD-S309 in the S309-bound Omicron spike protein (local refinement)

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)
Severe acute respiratory syndrome coronavirus 2 (Taxon ID: 2697049)

Expression System(s):

Homo sapiens

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.66 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:S309 neutralizing antibody he
Chain IDs:A, D (auth: C)
Chain Length:126
Number of Molecules:2
Biological Source:Homo sapiens

Polymer Type:polypeptide(L)
Molecule:S309 neutralizing antibody li
Chain IDs:B, E (auth: D)
Chain Length:108
Number of Molecules:2
Biological Source:Homo sapiens

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:C (auth: M), F (auth: E)
Chain Length:200
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF09408

Ligand Molecules

Primary Citation

Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape.

Zhao, Z, Zhou, J, Tian, M, Huang, M, Liu, S, Xie, Y, Han, P, Bai, C, Han, P, Zheng, A, Fu, L, Gao, Y, Peng, Q, Li, Y, Chai, Y, Zhang, Z, Zhao, X, Song, H, Qi, J, Wang, Q, Wang, P, Gao, G.F.Show

Nat Commun 13 4958 4958 (2022)

PMID: 36002453 DOI: 10.1038/s41467-022-32665-7

Abstact

Omicron SARS-CoV-2 is rapidly spreading worldwide. To delineate the impact of emerging mutations on spike's properties, we performed systematic structural analyses on apo Omicron spike and its complexes with human ACE2 or S309 neutralizing antibody (NAb) by cryo-EM. The Omicron spike preferentially adopts the one-RBD-up conformation both before and after ACE2 binding, which is in sharp contrast to the orchestrated conformational changes to create more up-RBDs upon ACE2 binding as observed in the prototype and other four variants of concern (VOCs). Furthermore, we found that S371L, S373P and S375F substitutions enhance the stability of the one-RBD-up conformation to prevent exposing more up-RBDs triggered by ACE2 binding. The increased stability of the one-RBD-up conformation restricts the accessibility of S304 NAb, which targets a cryptic epitope in the closed conformation, thus facilitating the immune evasion by Omicron. These results expand our understanding of Omicron spike's conformation, receptor binding and antibody evasion mechanism.

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Primary Citation of related structures

Abstact

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