7R9D

Crystal structure of Nb_0 in complex with Fab_8D3

7R9D の概要

• エントリーDOI: 10.2210/pdb7r9d/pdb
• 分子名称: Fab 8D3 light chain, Nanobody N0, Fab 8D3 heavy chain, ... (4 entities in total)
• 機能のキーワード: scaffold, protein binder, protein binding
• 由来する生物種: Mus musculus (Mouse); 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 61571.51

構造登録者

Wu, X.D.,Rapoport, T.A. (登録日: 2021-06-29, 公開日: 2021-10-06, 最終更新日: 2024-11-20)

主引用文献

Wu, X.,Rapoport, T.A.
Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies).
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: 1) a Fab fragment of an antibody directed against the nanobody and 2) a nanobody-binding protein A fragment fused to maltose binding protein and Fab-binding domains. The overall ensemble of ∼120 kDa, called Legobody, does not perturb the nanobody-target interaction, is easily recognizable in EM images due to its unique shape, and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23-kDa membrane protein, resulting in a map at 3.2-Å overall resolution with density sufficient for de novo model building, and for the 22-kDa receptor-binding domain (RBD) of SARS-CoV-2 spike protein, resulting in a map at 3.6-Å resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.

PubMed: 34620716
DOI: 10.1073/pnas.2115001118

実験手法

X-RAY DIFFRACTION (1.83 Å)