6EYC

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

Summary for 6EYC

• Entry DOI: 10.2210/pdb6eyc/pdb
• EMDB information: 6338
• Descriptor: DNA replication licensing factor MCM2, DNA replication licensing factor MCM3, DNA replication licensing factor MCM4, ... (8 entities in total)
• Functional Keywords: dna-directed dna polymerase, nucleus, multienzyme complex, nuclear protein
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 6
• Total formula weight: 609259.49

Authors

Croll, T.I. (deposition date: 2017-11-11, release date: 2018-06-20, Last modification date: 2024-05-08)

Primary citation

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

Experimental method

ELECTRON MICROSCOPY (3.8 Å)