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Instruments / Technical Area	Publication Details	Published
	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
I04-Macromolecular Crystallography	Accurate prediction of protein structures and interactions using a three-track neural network Minkyung Baek , Frank Dimaio , Ivan Anishchenko , Justas Dauparas , Sergey Ovchinnikov , Gyu Rie Lee , Jue Wang , Qian Cong , Lisa N. Kinch , R. Dustin Schaeffer , Claudia Millán , Hahnbeom Park , Carson Adams , Caleb R. Glassman , Andy Degiovanni , Jose H. Pereira , Andria V. Rodrigues , Alberdina A. Van Dijk , Ana C. Ebrecht , Diederik J. Opperman , Theo Sagmeister , Christoph Buhlheller , Tea Pavkov-Keller , Manoj K. Rathinaswamy , Udit Dalwadi , Calvin K. Yip , John E. Burke , K. Christopher Garcia , Nick V. Grishin , Paul D. Adams , Randy J. Read , David Baker Science 2 DOI: 10.1126/science.abj8754 Diamond Proposal Number(s): [20303] Show Abstract ▼ Abstract: DeepMind presented remarkably accurate predictions at the recent CASP14 protein structure prediction assessment conference. We explored network architectures incorporating related ideas and obtained the best performance with a three-track network in which information at the 1D sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging X-ray crystallography and cryo-EM structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short circuiting traditional approaches which require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research.	Jul 2021
Krios I-Titan Krios I at Diamond	Structure and lipid dynamics in the maintenance of lipid asymmetry inner membrane complex of A. baumannii Daniel Mann , Junping Fan , Kamolrat Somboon , Daniel P. Farrell , Andrew Muenks , Svetomir B. Tzokov , Frank Dimaio , Syma Khalid , Samuel I. Miller , Julien R. C. Bergeron Communications Biology 4 DOI: 10.1038/s42003-021-02318-4 Diamond Proposal Number(s): [19832] Open Access Show Abstract ▼ Abstract: Multi-resistant bacteria are a major threat in modern medicine. The gram-negative coccobacillus Acinetobacter baumannii currently leads the WHO list of pathogens in critical need for new therapeutic development. The maintenance of lipid asymmetry (MLA) protein complex is one of the core machineries that transport lipids from/to the outer membrane in gram-negative bacteria. It also contributes to broad-range antibiotic resistance in several pathogens, most prominently in A. baumannii. Nonetheless, the molecular details of its role in lipid transport has remained largely elusive. Here, we report the cryo-EM maps of the core MLA complex, MlaBDEF, from the pathogen A. baumannii, in the apo-, ATP- and ADP-bound states, revealing multiple lipid binding sites in the cytosolic and periplasmic side of the complex. Molecular dynamics simulations suggest their potential trajectory across the membrane. Collectively with the recently-reported structures of the E. coli orthologue, this data also allows us to propose a molecular mechanism of lipid transport by the MLA system.	Jun 2021
I02-Macromolecular Crystallography	Computational design of transmembrane pores Chunfu Xu , Peilong Lu , Tamer M. Gamal El-Din , Xue Y. Pei , Matthew C. Johnson , Atsuko Uyeda , Matthew J. Bick , Qi Xu , Daohua Jiang , Hua Bai , Gabriella Reggiano , Yang Hsia , T. J. Brunette , Jiayi Dou , Dan Ma , Eric M. Lynch , Scott E. Boyken , Po-Ssu Huang , Lance Stewart , Frank Dimaio , Justin M. Kollman , Ben Luisi , Tomoaki Matsuura , William A. Catterall , David Baker Nature 585, 129 - 134 DOI: 10.1038/s41586-020-2646-5 Diamond Proposal Number(s): [9537] Show Abstract ▼ Abstract: Transmembrane channels and pores have key roles in fundamental biological processes and in biotechnological applications such as DNA nanopore sequencing resulting in considerable interest in the design of pore-containing proteins. Synthetic amphiphilic peptides have been found to form ion channels, and there have been recent advances in de novo membrane protein design and in redesigning naturally occurring channel-containing proteins. However, the de novo design of stable, well-defined transmembrane protein pores that are capable of conducting ions selectively or are large enough to enable the passage of small-molecule fluorophores remains an outstanding challenge. Here we report the computational design of protein pores formed by two concentric rings of α-helices that are stable and monodisperse in both their water-soluble and their transmembrane forms. Crystal structures of the water-soluble forms of a 12-helical pore and a 16-helical pore closely match the computational design models. Patch-clamp electrophysiology experiments show that, when expressed in insect cells, the transmembrane form of the 12-helix pore enables the passage of ions across the membrane with high selectivity for potassium over sodium; ion passage is blocked by specific chemical modification at the pore entrance. When incorporated into liposomes using in vitro protein synthesis, the transmembrane form of the 16-helix pore—but not the 12-helix pore—enables the passage of biotinylated Alexa Fluor 488. A cryo-electron microscopy structure of the 16-helix transmembrane pore closely matches the design model. The ability to produce structurally and functionally well-defined transmembrane pores opens the door to the creation of designer channels and pores for a wide variety of applications.	Sep 2020
Krios III-Titan Krios III at Diamond	The cryo-EM structure of the bacterial flagellum cap complex suggests a molecular mechanism for filament elongation Natalie S. Al-Otaibi , Aidan J. Taylor , Daniel P. Farrell , Svetomir B. Tzokov , Frank Dimaio , David J. Kelly , Julien R. C. Bergeron Nature Communications 11 DOI: 10.1038/s41467-020-16981-4 Open Access Show Abstract ▼ Abstract: The bacterial flagellum is a remarkable molecular motor, whose primary function in bacteria is to facilitate motility through the rotation of a filament protruding from the bacterial cell. A cap complex, consisting of an oligomer of the protein FliD, is localized at the tip of the flagellum, and is essential for filament assembly, as well as adherence to surfaces in some bacteria. However, the structure of the intact cap complex, and the molecular basis for its interaction with the filament, remains elusive. Here we report the cryo-EM structure of the Campylobacter jejuni cap complex, which reveals that FliD is pentameric, with the N-terminal region of the protomer forming an extensive set of contacts across several subunits, that contribute to FliD oligomerization. We also demonstrate that the native C. jejuni flagellum filament is 11-stranded, contrary to a previously published cryo-EM structure, and propose a molecular model for the filament-cap interaction.	Jun 2020
Krios I-Titan Krios I at Diamond	Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus Serban L. Ilca , Xiaoyu Sun , Kamel El Omari , Abhay Kotecha , Felix De Haas , Frank Dimaio , Jonathan M. Grimes , David I. Stuart , Minna M. Poranen , Juha T. Huiskonen Nature 22 DOI: 10.1038/s41586-019-1229-9 Diamond Proposal Number(s): [14856] Show Abstract ▼ Abstract: Characterizing the genome of mature virions is pivotal to understanding the highly dynamic processes of virus assembly and infection. Owing to the different cellular fates of DNA and RNA, the life cycles of double-stranded (ds)DNA and dsRNA viruses are dissimilar. In terms of nucleic acid packing, dsDNA viruses, which lack genome segmentation and intra-capsid transcriptional machinery, predominantly display single-spooled genome organizations1,2,3,4,5,6,7,8. Because the release of dsRNA into the cytoplasm triggers host defence mechanisms9, dsRNA viruses retain their genomes within a core particle that contains the enzymes required for RNA replication and transcription10,11,12. The genomes of dsRNA viruses vary greatly in the degree of segmentation. In members of the Reoviridae family, genomes consist of 10–12 segments and exhibit a non-spooled arrangement mediated by RNA-dependent RNA polymerases11,12,13,14. However, whether this arrangement is a general feature of dsRNA viruses remains unknown. Here, using cryo-electron microscopy to resolve the dsRNA genome structure of the tri-segmented bacteriophage ɸ6 of the Cystoviridae family, we show that dsRNA viruses can adopt a dsDNA-like single-spooled genome organization. We find that in this group of viruses, RNA-dependent RNA polymerases do not direct genome ordering, and the dsRNA can adopt multiple conformations. We build a model that encompasses 90% of the genome, and use this to quantify variation in the packing density and to characterize the different liquid crystalline geometries that are exhibited by the tightly compacted nucleic acid. Our results demonstrate that the canonical model for the packing of dsDNA can be extended to dsRNA viruses.	May 2019
Krios I-Titan Krios I at Diamond	Structure of a chaperone-usher pilus reveals the molecular basis of rod uncoiling Manuela K. Hospenthal , Adam Redzej , Karen Dodson , Marta Ukleja , Brandon Frenz , Catarina Rodrigues , Scott j. Hultgren , Frank Dimaio , Edward h. Egelman , Gabriel Waksman Cell DOI: 10.1016/j.cell.2015.11.049 Diamond Proposal Number(s): [13256] Open Access Show Abstract ▼ Abstract: Type 1 and P pili are prototypical bacterial cell surface appendages playing essential roles in mediating recognition and adhesion of bacteria to the urinary tract. These pili, assembled by the chaperone-usher pathway, are polymers of pilus subunits assembling into two parts: a thin, short, tip fibrillum at the top, mounted on a long pilus rod. The rod adopts a helical quaternary structure and is thought to play essential roles: its formation may drive pilus extrusion by preventing backsliding of the nascent growing pilus within the secretion pore; the rod also has striking spring-like properties being able to uncoil and recoil depending on the intensity of shear forces generated by urine flow. Here we present an atomic model of the P pilus generated from a 3.8 Å resolution cryo-electron microscopy reconstruction. This structure provides the molecular basis for the rod’s remarkable mechanical properties and illuminates its role in pilus secretion.	Dec 2015
I24-Microfocus Macromolecular Crystallography	High thermodynamic stability of parametrically designed helical bundles P.-S. Huang , G. Oberdorfer , C. Xu , X. Y. Pei , B. L. Nannenga , J. M. Rogers , F. Dimaio , T. Gonen , B. Luisi , D. Baker Science 346 (6208), 481 - 485 DOI: 10.1126/science.1257481 PMID: 25342806 Show Abstract ▼ Abstract: We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil–generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated ΔGfold > 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.	Oct 2014

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