5VLV

The apo form of the triclocarban-binding single domain camelid nanobody VHH T9

5VLV の概要

• エントリーDOI: 10.2210/pdb5vlv/pdb
• 関連するPDBエントリー: 5VL2 5VM0 5VM4 5VM6
• 分子名称: Single Domain Camelid Nanobody VHH T9 (2 entities in total)
• 機能のキーワード: nanobody, triclocarban, unknown function
• 由来する生物種: Lama glama
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 14289.06

構造登録者

Tabares-da Rosa, S.,Gonzalez-Sapienza, G.,Wilson, D.K. (登録日: 2017-04-26, 公開日: 2018-05-02, 最終更新日: 2024-04-03)

主引用文献

Tabares-da Rosa, S.,Wogulis, L.A.,Wogulis, M.D.,Gonzalez-Sapienza, G.,Wilson, D.K.
Structure and specificity of several triclocarban-binding single domain camelid antibody fragments.
J. Mol. Recognit., 32:e2755-e2755, 2019

PubMed Abstract: The variable VHH domains of camelid single chain antibodies have been useful in numerous biotechnology applications due to their simplicity, biophysical properties, and abilities to bind to their cognate antigens with high affinities and specificity. Their interactions with proteins have been well-studied, but considerably less work has been done to characterize their ability to bind haptens. A high-resolution structural study of three nanobodies (T4, T9, and T10) which have been shown to bind triclocarban (TCC, 3-(4-chlorophenyl)-1-(3,4-dichlorophenyl)urea) with near-nanomolar affinity shows that binding occurs in a tunnel largely formed by CDR1 rather than a surface or lateral binding mode seen in other nanobody-hapten interactions. Additional significant interactions are formed with a non-hypervariable loop, sometimes dubbed "CDR4". A comparison of apo and holo forms of T9 and T10 shows that the binding site undergoes little conformational change upon binding of TCC. Structures of three nanobody-TCC complexes demonstrated there was not a standard binding mode. T4 and T9 have a high degree of sequence identity and bind the hapten in a nearly identical manner, while the more divergent T10 binds TCC in a slightly displaced orientation with the urea moiety rotated approximately 180° along the long axis of the molecule. In addition to methotrexate, this is the second report of haptens binding in a tunnel formed by CDR1, suggesting that compounds with similar hydrophobicity and shape could be recognized by nanobodies in analogous fashion. Structure-guided mutations failed to improve binding affinity for T4 and T9 underscoring the high degree of natural optimization.

PubMed: 30033524
DOI: 10.1002/jmr.2755

実験手法

X-RAY DIFFRACTION (1.35 Å)