7Z9R

CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 2Up1Down conformation

7Z9R の概要

• エントリーDOI: 10.2210/pdb7z9r/pdb
• 関連するPDBエントリー: 7Z6V 7Z7X 7Z85 7Z86 7Z9Q
• EMDBエントリー: 14576
• 分子名称: Spike glycoprotein,Fibritin, Nanobody H11-H4 Q98R H100E, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• 機能のキーワード: complex, spike glycoprotein, nanobody h11-h4 q98r h100e, antiviral protein
• 由来する生物種: Severe acute respiratory syndrome coronavirus 2; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 476196.32

構造登録者

Weckener, M.,Naismith, J.H. (登録日: 2022-03-21, 公開日: 2022-07-13, 最終更新日: 2022-10-05)

主引用文献

Mikolajek, H.,Weckener, M.,Brotzakis, Z.F.,Huo, J.,Dalietou, E.V.,Le Bas, A.,Sormanni, P.,Harrison, P.J.,Ward, P.N.,Truong, S.,Moynie, L.,Clare, D.K.,Dumoux, M.,Dormon, J.,Norman, C.,Hussain, N.,Vogirala, V.,Owens, R.J.,Vendruscolo, M.,Naismith, J.H.
Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.
Proc.Natl.Acad.Sci.USA, 119:e2205412119-e2205412119, 2022

PubMed Abstract: Camelid single-domain antibodies, also known as nanobodies, can be readily isolated from naïve libraries for specific targets but often bind too weakly to their targets to be immediately useful. Laboratory-based genetic engineering methods to enhance their affinity, termed maturation, can deliver useful reagents for different areas of biology and potentially medicine. Using the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and a naïve library, we generated closely related nanobodies with micromolar to nanomolar binding affinities. By analyzing the structure-activity relationship using X-ray crystallography, cryoelectron microscopy, and biophysical methods, we observed that higher conformational entropy losses in the formation of the spike protein-nanobody complex are associated with tighter binding. To investigate this, we generated structural ensembles of the different complexes from electron microscopy maps and correlated the conformational fluctuations with binding affinity. This insight guided the engineering of a nanobody with improved affinity for the spike protein.

PubMed: 35858383
DOI: 10.1073/pnas.2205412119

実験手法

ELECTRON MICROSCOPY (4.2 Å)