7MFU

Crystal structure of synthetic nanobody (Sb14+Sb68) complexes with SARS-CoV-2 receptor binding domain

7MFU の概要

• エントリーDOI: 10.2210/pdb7mfu/pdb
• 関連するPDBエントリー: 7KGJ 7KGK 7KGL 7KLW
• 分子名称: Spike protein S1, Synthetic Nanobody #14 (Sb14), Synthetic nanobody #68 (Sb68), ... (6 entities in total)
• 機能のキーワード: sars-cov-2, spike protein, receptor binding domain, rbd, antibody, nanobody, sybody, complex, neutralization, viral protein, epitope
• 由来する生物種: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2); 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 97302.57

構造登録者

Jiang, J.,Ahmad, J.,Natarajan, K.,Boyd, L.F.,Margulies, D.H. (登録日: 2021-04-11, 公開日: 2021-06-02, 最終更新日: 2024-11-06)

主引用文献

Ahmad, J.,Jiang, J.,Boyd, L.F.,Zeher, A.,Huang, R.,Xia, D.,Natarajan, K.,Margulies, D.H.
Structures of synthetic nanobody-SARS-CoV-2 receptor-binding domain complexes reveal distinct sites of interaction.
J.Biol.Chem., 297:101202-101202, 2021

PubMed Abstract: Combating the worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the emergence of new variants demands understanding of the structural basis of the interaction of antibodies with the SARS-CoV-2 receptor-binding domain (RBD). Here, we report five X-ray crystal structures of sybodies (synthetic nanobodies) including those of binary and ternary complexes of Sb16-RBD, Sb45-RBD, Sb14-RBD-Sb68, and Sb45-RBD-Sb68, as well as unliganded Sb16. These structures reveal that Sb14, Sb16, and Sb45 bind the RBD at the angiotensin-converting enzyme 2 interface and that the Sb16 interaction is accompanied by a large conformational adjustment of complementarity-determining region 2. In contrast, Sb68 interacts at the periphery of the SARS-CoV-2 RBD-angiotensin-converting enzyme 2 interface. We also determined cryo-EM structures of Sb45 bound to the SARS-CoV-2 spike protein. Superposition of the X-ray structures of sybodies onto the trimeric spike protein cryo-EM map indicates that some sybodies may bind in both "up" and "down" configurations, but others may not. Differences in sybody recognition of several recently identified RBD variants are explained by these structures.

PubMed: 34537245
DOI: 10.1016/j.jbc.2021.101202

実験手法

X-RAY DIFFRACTION (1.7 Å)