학술논문
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge
Document Type
Article
Author
Lawson, Catherine L.; Kryshtafovych, Andriy; Pintilie, Grigore D.; Burley, Stephen K.; Černý, Jiří; Chen, Vincent B.; Emsley, Paul; Gobbi, Alberto; Joachimiak, Andrzej; Noreng, Sigrid; Prisant, Michael G.; Read, Randy J.; Richardson, Jane S.; Rohou, Alexis L.; Schneider, Bohdan; Sellers, Benjamin D.; Shao, Chenghua; Sourial, Elizabeth; Williams, Chris I.; Williams, Christopher J.; Yang, Ying; Abbaraju, Venkat; Afonine, Pavel V.; Baker, Matthew L.; Bond, Paul S.; Blundell, Tom L.; Burnley, Tom; Campbell, Arthur; Cao, Renzhi; Cheng, Jianlin; Chojnowski, Grzegorz; Cowtan, K. D.; DiMaio, Frank; Esmaeeli, Reza; Giri, Nabin; Grubmüller, Helmut; Hoh, Soon Wen; Hou, Jie; Hryc, Corey F.; Hunte, Carola; Igaev, Maxim; Joseph, Agnel P.; Kao, Wei-Chun; Kihara, Daisuke; Kumar, Dilip; Lang, Lijun; Lin, Sean; Maddhuri Venkata Subramaniya, Sai R.; Mittal, Sumit; Mondal, Arup; Moriarty, Nigel W.; Muenks, Andrew; Murshudov, Garib N.; Nicholls, Robert A.; Olek, Mateusz; Palmer, Colin M.; Perez, Alberto; Pohjolainen, Emmi; Pothula, Karunakar R.; Rowley, Christopher N.; Sarkar, Daipayan; Schäfer, Luisa U.; Schlicksup, Christopher J.; Schröder, Gunnar F.; Shekhar, Mrinal; Si, Dong; Singharoy, Abhishek; Sobolev, Oleg V.; Terashi, Genki; Vaiana, Andrea C.; Vedithi, Sundeep C.; Verburgt, Jacob; Wang, Xiao; Warshamanage, Rangana; Winn, Martyn D.; Weyand, Simone; Yamashita, Keitaro; Zhao, Minglei; Schmid, Michael F.; Berman, Helen M.; Chiu, Wah
Source
Nature Methods; 20240101, Issue: Preprints p1-9, 9p
Subject
Language
ISSN
15487091; 15487105
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 colibeta-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.