6EYC

Re-refinement of the MCM2-7 double hexamer using ISOLDE

6EYC の概要

• エントリーDOI: 10.2210/pdb6eyc/pdb
• EMDBエントリー: 6338
• 分子名称: DNA replication licensing factor MCM2, DNA replication licensing factor MCM3, DNA replication licensing factor MCM4, ... (8 entities in total)
• 機能のキーワード: dna-directed dna polymerase, nucleus, multienzyme complex, nuclear protein
• 由来する生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 609259.49

構造登録者

Croll, T.I. (登録日: 2017-11-11, 公開日: 2018-06-20, 最終更新日: 2024-05-08)

主引用文献

Croll, T.I.
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Acta Crystallogr D Struct Biol, 74:519-530, 2018

PubMed Abstract: This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron-density maps. ISOLDE combines interactive molecular-dynamics flexible fitting with modern molecular-graphics visualization and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.

PubMed: 29872003
DOI: 10.1107/S2059798318002425

実験手法

ELECTRON MICROSCOPY (3.8 Å)