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.

• MeSH
• beta-galaktosidasa chemie   metabolismus   MeSH
• COVID-19 virologie   MeSH
• elektronová kryomikroskopie * metody   MeSH
• Escherichia coli MeSH
• konformace proteinů MeSH
• ligandy MeSH
• molekulární modely * MeSH
• reprodukovatelnost výsledků MeSH
• SARS-CoV-2 MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• beta-galaktosidasa MeSH
• ligandy MeSH

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: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. We found that (1) the quality of submitted ligand models and surrounding atoms varied, as judged by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics, and contact scores, and (2) 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.

• Publikační typ
• časopisecké články MeSH
• preprinty MeSH

Structural knowledge of biological macromolecules is essential for understanding their function and for modifying that function by engineering. Protein crystallography is a powerful method for elucidating molecular structures of proteins, but it is essential that the investigator has a basic knowledge of good practices and of the major pitfalls in the technique. Here we describe issues specific for the case of structural studies of strigolactone (SL) receptor structure and function, and in particular the difficulties associated with capturing complexes of SL receptors with the SL hormone ligand in the crystal.

• Klíčová slova
• Crystallization, Ligand binding, Macromolecular crystallography, Strigolactone, Strigolactone receptors,
• MeSH
• heterocyklické sloučeniny tricyklické metabolismus   MeSH
• konformace proteinů MeSH
• krystalografie rentgenová MeSH
• laktony metabolismus   MeSH
• ligandy MeSH
• molekulární modely MeSH
• receptory buněčného povrchu genetika   metabolismus   MeSH
• regulace genové exprese u rostlin MeSH
• rostlinné proteiny genetika   metabolismus   MeSH
• signální transdukce MeSH
• vazba proteinů MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• GR24 strigolactone MeSH Prohlížeč
• heterocyklické sloučeniny tricyklické MeSH
• laktony MeSH
• ligandy MeSH
• receptory buněčného povrchu MeSH
• rostlinné proteiny MeSH

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) play a crucial role in structure-guided drug discovery and design, and also provide atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. The quality with which small-molecule ligands have been modelled in Protein Data Bank (PDB) entries has been, and continues to be, a matter of concern for many investigators. Correctly interpreting whether electron density found in a binding site is compatible with the soaked or co-crystallized ligand or represents water or buffer molecules is often far from trivial. The Worldwide PDB validation report (VR) provides a mechanism to highlight any major issues concerning the quality of the data and the model at the time of deposition and annotation, so the depositors can fix issues, resulting in improved data quality. The ligand-validation methods used in the generation of the current VRs are described in detail, including an examination of the metrics to assess both geometry and electron-density fit. It is found that the LLDF score currently used to identify ligand electron-density fit outliers can give misleading results and that better ligand-validation metrics are required.

• Klíčová slova
• PDB, Protein Data Bank, ligands, three-dimensional macromolecular structure, validation,
• MeSH
• databáze proteinů * MeSH
• konformace proteinů * MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• ligandy MeSH
• makromolekulární látky chemie   MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• proteiny analýza   chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• validační studie MeSH
• Názvy látek
• ligandy MeSH
• makromolekulární látky MeSH
• proteiny MeSH