9P55

Structure of DNA-free long form XPD from Thermoplasma acidophilum

Summary for 9P55

• Entry DOI: 10.2210/pdb9p55/pdb
• Descriptor: ATP-dependent DNA helicase XPD, IRON/SULFUR CLUSTER, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: helicase, atpase, dna binding protein, hydrolase
• Biological source: Thermoplasma acidophilum DSM 1728
• Total number of polymer chains: 1
• Total formula weight: 74898.93

Authors

Bravo, M.,Fan, L. (deposition date: 2025-06-17, release date: 2026-01-21, Last modification date: 2026-02-11)

Primary citation

Bravo, M.,Fan, L.
A new crystal form of the DNA-free full-length XPD helicase from Thermoplasma acidophilum.
Acta Crystallogr.,Sect.F, 82:42-48, 2026

PubMed Abstract: The XPD helicase plays a critical role in DNA repair and serves as a model for structural studies of superfamily 2 (SF2) helicases. We report a novel orthorhombic crystal form of DNA-free Thermoplasma acidophilum XPD (TaXPD) obtained under high ionic strength conditions generated by sodium potassium tartrate and NaCl-based vapor-diffusion conditions, in contrast to earlier previously reported conditions that used polyols (PEG) or diols (MPD). The crystals belonged to space group P222 (a = 59.53, b = 96.00, c = 159.09 Å) and diffracted to 2.13 Å resolution, yielding the highest resolution TaXPD structure to date. Structural analysis showed that this crystal form contains fewer intermolecular interfaces than the previously reported hexagonal lattice, as supported by Protein Interfaces, Surfaces and Assemblies (PISA) analysis. This supports the determination of the 510-514 loop in the long-form DNA-free TaXPD, which was previously disordered in other structures. This work highlights how crystallization conditions influence lattice organization, structural completeness and diffraction quality. In this structure, Tyr425 adopts a conformation that may regulate DNA access in the DNA-free state.

PubMed: 41528811
DOI: 10.1107/S2053230X26000105

Experimental method

X-RAY DIFFRACTION (2.127 Å)