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Instruments / Technical Area	Publication Details	Published
Krios I-Titan Krios I at Diamond Krios II-Titan Krios II at Diamond Krios III-Titan Krios III at Diamond	CryoET structures of immature HIV Gag reveal six-helix bundle Luiza Mendonca , Dapeng Sun , Jiying Ning , Jiwei Liu , Abhay Kotecha , Mateusz Olek , Thomas Frosio , Xiaofeng Fu , Benjamin A. Himes , Alex B. Kleinpeter , Eric O. Freed , Jing Zhou , Christopher Aiken , Peijun Zhang Communications Biology 4 DOI: 10.1038/s42003-021-01999-1 Diamond Proposal Number(s): [18477, 21005, 21004] Open Access Show Abstract ▼ Abstract: Gag is the HIV structural precursor protein which is cleaved by viral protease to produce mature infectious viruses. Gag is a polyprotein composed of MA (matrix), CA (capsid), SP1, NC (nucleocapsid), SP2 and p6 domains. SP1, together with the last eight residues of CA, have been hypothesized to form a six-helix bundle responsible for the higher-order multimerization of Gag necessary for HIV particle assembly. However, the structure of the complete six-helix bundle has been elusive. Here, we determined the structures of both Gag in vitro assemblies and Gag viral-like particles (VLPs) to 4.2 Å and 4.5 Å resolutions using cryo-electron tomography and subtomogram averaging by emClarity. A single amino acid mutation (T8I) in SP1 stabilizes the six-helix bundle, allowing to discern the entire CA-SP1 helix connecting to the NC domain. These structures provide a blueprint for future development of small molecule inhibitors that can lock SP1 in a stable helical conformation, interfere with virus maturation, and thus block HIV-1 infection.	Apr 2021
	Atomic model validation using the CCP-EM software suite Agnel Praveen Joseph , Mateusz Olek , Sony Malhotra , Peijun Zhang , Kevin Cowtan , Tom Burnley , Martyn Winn Acta Crystallographica Section D Structural Biology 78 DOI: 10.1107/S205979832101278X Open Access Show Abstract ▼ Abstract: Recently, there has been a dramatic improvement in the quality and quantity of data derived using cryogenic electron microscopy (cryo-EM). This is also associated with a large increase in the number of atomic models built. Although the best resolutions that are achievable are improving, often the local resolution is variable, and a significant majority of data are still resolved at resolutions worse than 3 Å. Model building and refinement is often challenging at these resolutions, and hence atomic model validation becomes even more crucial to identify less reliable regions of the model. Here, a graphical user interface for atomic model validation, implemented in the CCP-EM software suite, is presented. It is aimed to develop this into a platform where users can access multiple complementary validation metrics that work across a range of resolutions and obtain a summary of evaluations. Based on the validation estimates from atomic models associated with cryo-EM structures from SARS-CoV-2, it was observed that models typically favor adopting the most common conformations over fitting the observations when compared with the model agreement with data. At low resolutions, the stereochemical quality may be favored over data fit, but care should be taken to ensure that the model agrees with the data in terms of resolvable features. It is demonstrated that further re-refinement can lead to improvement of the agreement with data without the loss of geometric quality. This also highlights the need for improved resolution-dependent weight optimization in model refinement and an effective test for overfitting that would help to guide the refinement process.	Feb 2022
	IceBreaker: Software for high-resolution single-particle cryo-EM with non-uniform ice Mateusz Olek , Kevin Cowtan , Donovan Webb , Yuriy Chaban , Peijun Zhang Structure 43 DOI: 10.1016/j.str.2022.01.005 Open Access Show Abstract ▼ Abstract: Despite the abundance of available software tools, optimal particle selection is still a vital issue in single-particle cryoelectron microscopy (cryo-EM). Regardless of the method used, most pickers struggle when ice thickness varies on a micrograph. IceBreaker allows users to estimate the relative ice gradient and flatten it by equalizing the local contrast. It allows the differentiation of particles from the background and improves overall particle picking performance. Furthermore, we introduce an additional parameter corresponding to local ice thickness for each particle. Particles with a defined ice thickness can be grouped and filtered based on this parameter during processing. These functionalities are especially valuable for on-the-fly processing to automatically pick as many particles as possible from each micrograph and to select optimal regions for data collection. Finally, estimated ice gradient distributions can be stored separately and used to inspect the quality of prepared samples.	Feb 2022
	Outcomes of the EMDataResource cryo-EM ligand modeling challenge Catherine L. Lawson , Andriy Kryshtafovych , Grigore D. Pintilie , Stephen Burley , Jiří Černý , Vincent B. Chen , Paul Emsley , Alberto Gobbi , Andrzej Joachimiak , Sigrid Noreng , Michael G. Prisant , Randy J. Read , Jane S. Richardson , Alexis L. Rohou , Bohdan Schneider , Benjamin D. Sellers , Chenghua Shao , Elizabeth Sourial , Chris I. Williams , Christopher J. Williams , Ying Yang , Venkat Abbaraju , Pavel V. Afonine , Matthew L. Baker , Paul S. Bond , Tom L. Blundell , Tom Burnley , Arthur Campbell , Renzhi Cao , Jianlin Cheng , Grzegorz Chojnowski , Kevin D. Cowtan , Frank Dimaio , Reza Esmaeeli , Nabin Giri , Helmut Grubmüller , Soon Wen Hoh , Jie Hou , Corey F. Hryc , Carola Hunte , Maxim Igaev , Agnel P. Joseph , Wei-Chun Kao , Daisuke Kihara , Dilip Kumar , Lijun Lang , Sean Lin , Sai R. Maddhuri Venkata Subramaniya , Sumit Mittal , Arup Mondal , Nigel W. Moriarty , Andrew Muenks , Garib N. Murshudov , Robert A. Nicholls , Mateusz Olek , Colin M. Palmer , Alberto Perez , Emmi Pohjolainen , Karunakar R. Pothula , Christopher N. Rowley , Daipayan Sarkar , Luisa U. Schäfer , Christopher J. Schlicksup , Gunnar F. Schröder , Mrinal Shekhar , Dong Si , Abhishek Singharoy , Oleg V. Sobolev , Genki Terashi , Andrea C. Vaiana , Sundeep C. Vedithi , Jacob Verburgt , Xiao Wang , Rangana Warshamanage , Martyn Winn , Simone Weyand , Keitaro Yamashita , Minglei Zhao , Michael F. Schmid , Helen M. Berman , Wah Chiu Nature Methods 24 DOI: 10.1038/s41592-024-02321-7 Show Abstract ▼ 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.	Jun 2024

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