Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase,Acta Crystallographica Section D

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Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase
Acta Crystallographica Section D ( IF 2.6 ) Pub Date : 2024-02-02 , DOI: 10.1107/s205979832400038x
Marlo K Thompson ₁ , Nidhi Sharma ₁ , Andrea Thorn ₂ , Aishwarya Prakash ₁

Affiliation

Nanobodies (VHHs) are single-domain antibodies with three antigenic CDR regions and are used in diverse scientific applications. Here, an ∼14 kDa nanobody (A5) specific for the endonuclease VIII (Nei)-like 1 or NEIL1 DNA glycosylase involved in the first step of the base-excision repair pathway was crystallized and its structure was determined to 2.1 Å resolution. The crystals posed challenges due to potential twinning and anisotropic diffraction. Despite inconclusive twinning indicators, reprocessing in an orthorhombic setting and molecular replacement in space group P2₁2₁2 enabled the successful modeling of 96% of residues in the asymmetric unit, with final R_work and R_free values of 0.199 and 0.229, respectively.

中文翻译：

破译针对 NEIL1 DNA 糖基化酶的新型纳米抗体的晶体结构

纳米抗体 (VHH) 是具有三个抗原 CDR 区域的单域抗体，可用于多种科学应用。在此，对参与碱基切除修复途径第一步的核酸内切酶 VIII (Nei) 样 1 或 NEIL1 DNA 糖基化酶具有特异性的~14 kDa 纳米抗体 (A5) 结晶，并以 2.1 Å 分辨率确定了其结构。由于潜在的孪生和各向异性衍射，晶体带来了挑战。尽管孪生指标尚无定论，但在斜方晶格环境中进行后处理以及在空间群P 2 ₁ 2 ₁ 2 中进行分子置换，成功地对不对称单元中 96% 的残基进行了建模，最终R_功和R_游离值分别为 0.199 和 0.229 。

更新日期：2024-02-02

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