ISDA

Deposition Date 2022-05-26

Release Date 2022-09-28

Last Version Date 2024-10-23

Entry Detail

PDB ID:

7XWA

Keywords:

VIRAL PROTEIN

Title:

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.4/5 variant spike protein in complex with its receptor ACE2

Biological Source:

Source Organism:

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

Host Organism:

Homo sapiens

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.36 Å

R-Value Free:

0.28

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 1 21 1

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Processed angiotensin-converting enzyme 2
Gene (Uniprot):ACE2
Chain IDs:A, C
Chain Length:608
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q9BYF1 Pfam ID:PF01401 EC:3.4.15.1

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:B, D
Chain Length:234
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2

UniProt ID:P0DTC2 Pfam ID:PF09408

Ligand Molecules

NAG

Primary Citation

Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5.

Kimura, I, Yamasoba, D, Tamura, T, Nao, N, Suzuki, T, Oda, Y, Mitoma, S, Ito, J, Nasser, H, Zahradnik, J, Uriu, K, Fujita, S, Kosugi, Y, Wang, L, Tsuda, M, Kishimoto, M, Ito, H, Suzuki, R, Shimizu, R, Begum, M.M, Yoshimatsu, K, Kimura, K.T, Sasaki, J, Sasaki-Tabata, K, Yamamoto, Y, Nagamoto, T, Kanamune, J, Kobiyama, K, Asakura, H, Nagashima, M, Sadamasu, K, Yoshimura, K, Shirakawa, K, Takaori-Kondo, A, Kuramochi, J, Schreiber, G, Ishii, K.J, Hashiguchi, T, Ikeda, T, Saito, A, Fukuhara, T, Tanaka, S, Matsuno, K, Sato, K.Show

Cell 185 3992 ? (2022)

PMID: 36198317 DOI: 10.1016/j.cell.2022.09.018

Abstact

After the global spread of the SARS-CoV-2 Omicron BA.2, some BA.2 subvariants, including BA.2.9.1, BA.2.11, BA.2.12.1, BA.4, and BA.5, emerged in multiple countries. Our statistical analysis showed that the effective reproduction numbers of these BA.2 subvariants are greater than that of the original BA.2. Neutralization experiments revealed that the immunity induced by BA.1/2 infections is less effective against BA.4/5. Cell culture experiments showed that BA.2.12.1 and BA.4/5 replicate more efficiently in human alveolar epithelial cells than BA.2, and particularly, BA.4/5 is more fusogenic than BA.2. We further provided the structure of the BA.4/5 spike receptor-binding domain that binds to human ACE2 and considered how the substitutions in the BA.4/5 spike play roles in ACE2 binding and immune evasion. Moreover, experiments using hamsters suggested that BA.4/5 is more pathogenic than BA.2. Our multiscale investigations suggest that the risk of BA.2 subvariants, particularly BA.4/5, to global health is greater than that of original BA.2.

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Primary Citation of related structures