8H7N

Structure of nanobody 11A in complex with triazophos

Summary for 8H7N

• Entry DOI: 10.2210/pdb8h7n/pdb
• Related: 8H7I 8H7M 8H7R
• Descriptor: Nanobody 11A, 1,2-ETHANEDIOL, triazophos, ... (5 entities in total)
• Functional Keywords: nanobody, organophosphorus pesticide, immune system
• Biological source: Camelus bactrianus (Bactrian camel)
• Total number of polymer chains: 1
• Total formula weight: 15712.15

Authors

Wang, H.,Li, J.D.,Shen, X.,Xu, Z.L.,Sun, Y.M. (deposition date: 2022-10-20, release date: 2023-10-25, Last modification date: 2025-04-02)

Primary citation

Li, J.D.,Wu, G.P.,Li, L.H.,Wang, L.T.,Liang, Y.F.,Fang, R.Y.,Zhang, Q.L.,Xie, L.L.,Shen, X.,Shen, Y.D.,Xu, Z.L.,Wang, H.,Hammock, B.D.
Structural Insights into the Stability and Recognition Mechanism of the Antiquinalphos Nanobody for the Detection of Quinalphos in Foods.
Anal.Chem., 95:11306-11315, 2023

PubMed Abstract: Nanobodies (Nbs) have great potential in immunoassays due to their exceptional physicochemical properties. With the immortal nature of Nbs and the ability to manipulate their structures using protein engineering, it will become increasingly valuable to understand what structural features of Nbs drive high stability, affinity, and selectivity. Here, we employed an anti-quinalphos Nb as a model to illustrate the structural basis of Nbs' distinctive physicochemical properties and the recognition mechanism. The results indicated that the Nb-11A-ligand complexes exhibit a "tunnel" binding mode formed by CDR1, CDR2, and FR3. The orientation and hydrophobicity of small ligands are the primary determinants of their diverse affinities to Nb-11A. In addition, the primary factors contributing to Nb-11A's limited stability at high temperatures and in organic solvents are the rearrangement of the hydrogen bonding network and the enlargement of the binding cavity. Importantly, Ala 97 and Ala 34 at the active cavity's bottom and Arg 29 and Leu 73 at its entrance play vital roles in hapten recognition, which were further confirmed by mutant Nb-F3. Thus, our findings contribute to a deeper understanding of the recognition and stability mechanisms of anti-hapten Nbs and shed new light on the rational design of novel haptens and directed evolution to produce high-performance antibodies.

PubMed: 37428097
DOI: 10.1021/acs.analchem.3c01370

Experimental method

X-RAY DIFFRACTION (1.99 Å)