ISDA

Entry Detail

PDB ID:

8FTT

Keywords:

PROTEIN BINDING

Title:

Crystal structure of a glycosylase specific nanobody

Biological Source:

Source Organism:

synthetic construct

Host Organism:

Escherichia coli BL21(DE3)

PDB Version:

Deposition Date:

2023-01-13

Release Date:

2023-10-11

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.08 Å

R-Value Free:

0.22

R-Value Work:

0.19

R-Value Observed:

0.25

Space Group:

P 21 21 2

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Macromolecular Entities

Polymer Type:polypeptide(L)
Description:Anti-NEIL1 Nanobody
Chain IDs:A, B, C, D
Chain Length:130
Number of Molecules:4
Biological Source:synthetic construct

Ligand Molecules

SO4

Primary Citation

Deciphering the crystal structure of a novel nanobody against the NEIL1 DNA glycosylase.

Thompson, M.K, Sharma, N, Thorn, A, Prakash, A, Thompson, M.K, Sharma, N, Prakash, A.Show

Acta Crystallogr D Struct Biol 80 137 146 (2024)

PMID: 38289715 DOI: 10.1107/S205979832400038X

Abstact

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 Rwork and Rfree values of 0.199 and 0.229, respectively.

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Primary Citation of related structures