8SPL

Proteinase K Multiconformer Model at 343K

8SPL の概要

• エントリーDOI: 10.2210/pdb8spl/pdb
• 関連するPDBエントリー: 8sog 8sou 8sov
• 分子名称: Proteinase K, ALA-ALA-ALA-SER-VAL-LYS, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: serine hydrolase, subtilisin-like, metal ion binding, a/b three-layered sandwiches, hydrolase
• 由来する生物種: Parengyodontium album; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 29833.69

構造登録者

Du, S.,Wankowicz, S.,Yabukarski, F.,Doukov, T.,Herschlag, D.,Fraser, J.S. (登録日: 2023-05-03, 公開日: 2023-08-09, 最終更新日: 2024-10-30)

主引用文献

Du, S.,Wankowicz, S.A.,Yabukarski, F.,Doukov, T.,Herschlag, D.,Fraser, J.S.
Refinement of multiconformer ensemble models from multi-temperature X-ray diffraction data.
Methods Enzymol., 688:223-254, 2023

PubMed Abstract: Conformational ensembles underlie all protein functions. Thus, acquiring atomic-level ensemble models that accurately represent conformational heterogeneity is vital to deepen our understanding of how proteins work. Modeling ensemble information from X-ray diffraction data has been challenging, as traditional cryo-crystallography restricts conformational variability while minimizing radiation damage. Recent advances have enabled the collection of high quality diffraction data at ambient temperatures, revealing innate conformational heterogeneity and temperature-driven changes. Here, we used diffraction datasets for Proteinase K collected at temperatures ranging from 313 to 363 K to provide a tutorial for the refinement of multiconformer ensemble models. Integrating automated sampling and refinement tools with manual adjustments, we obtained multiconformer models that describe alternative backbone and sidechain conformations, their relative occupancies, and interconnections between conformers. Our models revealed extensive and diverse conformational changes across temperature, including increased bound peptide ligand occupancies, different Ca binding site configurations and altered rotameric distributions. These insights emphasize the value and need for multiconformer model refinement to extract ensemble information from diffraction data and to understand ensemble-function relationships.

PubMed: 37748828
DOI: 10.1016/bs.mie.2023.06.009

実験手法

X-RAY DIFFRACTION (1.21 Å)