Children’s Nutrition Research Center Staff Publications
Language
English
Publication Date
7-1-2024
Journal
Nature Methods
DOI
10.1038/s41592-024-02321-7
PMID
38918604
PMCID
PMC11526832
PubMedCentral® Posted Date
1-1-2025
PubMedCentral® Full Text Version
Author MSS
Abstract
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contact scores. A composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
Keywords
Cryoelectron Microscopy, Ligands, Models, Molecular, SARS-CoV-2, COVID-19, Escherichia coli, beta-Galactosidase, Protein Conformation, Reproducibility of Results
Published Open-Access
yes
Recommended Citation
Lawson, Catherine L; Kryshtafovych, Andriy; Pintilie, Grigore D; et al., "Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge" (2024). Children’s Nutrition Research Center Staff Publications. 308.
https://digitalcommons.library.tmc.edu/staff_pub/308
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Biochemical Phenomena, Metabolism, and Nutrition Commons, Dietetics and Clinical Nutrition Commons, Endocrinology, Diabetes, and Metabolism Commons, Nutrition Commons