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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
I03-Macromolecular Crystallography	Target highlights in CASP14 : Analysis of models by structure providers Leila T. Alexander , Rosalba Lepore , Andriy Kryshtafovych , Athanasios Adamopoulos , Markus Alahuhta , Ann M. Arvin , Yannick J. Bomble , Bettina Böttcher , Cécile Breyton , Valerio Chiarini , Naga Babu Chinnam , Wah Chiu , Krzysztof Fidelis , Rhys Grinter , Gagan D. Gupta , Marcus D. Hartmann , Christopher S. Hayes , Tatjana Heidebrecht , Andrea Ilari , Andrzej Joachimiak , Youngchang Kim , Romain Linares , Andrew L. Lovering , Vladimir V. Lunin , Andrei N. Lupas , Cihan Makbul , Karolina Michalska , John Moult , Prasun K. Mukherjee , William Nutt , Stefan L. Oliver , Anastassis Perrakis , Lucy Stols , John A. Tainer , Maya Topf , Susan E. Tsutakawa , Mauricio Valdivia‐delgado , Torsten Schwede Proteins: Structure, Function, And Bioinformatics 89, 1647 - 1672 DOI: 10.1002/prot.26247 Open Access Show Abstract ▼ Abstract: The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.	Dec 2021
	REMBI: Recommended Metadata for Biological Images—enabling reuse of microscopy data in biology Ugis Sarkans , Wah Chiu , Lucy M. Collinson , Michele C. Darrow , Jan Ellenberg , David Grunwald , Jean-Karim Hériché , Andrii Iudin , Gabriel G. Martins , Terry Meehan , Kedar Narayan , Ardan Patwardhan , Matthew Robert Geoffrey Russell , Helen R. Saibil , Caterina Strambio-De-Castillia , Jason R. Swedlow , Christian Tischer , Virginie Uhlmann , Paul Verkade , Mary Barlow , Omer Bayraktar , Ewan Birney , Cesare Catavitello , Christopher Cawthorne , Stephan Wagner-Conrad , Elizabeth Duke , Perrine Paul-Gilloteaux , Emmanuel Gustin , Maria Harkiolaki , Pasi Kankaanpää , Thomas Lemberger , Jo Mcentyre , Josh Moore , Andrew W. Nicholls , Shuichi Onami , Helen Parkinson , Maddy Parsons , Marina Romanchikova , Nicholas Sofroniew , Jim Swoger , Nadine Utz , Lenard M. Voortman , Frances Wong , Peijun Zhang , Gerard J. Kleywegt , Alvis Brazma Nature Methods 21 DOI: 10.1038/s41592-021-01166-8 Show Abstract ▼ Abstract: Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.	May 2021
Talos-Talos Arctica at Diamond	Machining protein microcrystals for structure determination by electron diffraction Helen M. E. Duyvesteyn , Abhay Kotecha , Helen M. Ginn , Corey W. Hecksel , Emma V. Beale , Felix De Haas , Gwyndaf Evans , Peijun Zhang , Wah Chiu , David I. Stuart Proceedings Of The National Academy Of Sciences 74 DOI: 10.1073/pnas.1809978115 Open Access Show Abstract ▼ Abstract: We demonstrate that ion-beam milling of frozen, hydrated protein crystals to thin lamella preserves the crystal lattice to near-atomic resolution. This provides a vehicle for protein structure determination, bridging the crystal size gap between the nanometer scale of conventional electron diffraction and micron scale of synchrotron microfocus beamlines. The demonstration that atomic information can be retained suggests that milling could provide such detail on sections cut from vitrified cells.	Aug 2018
I24-Microfocus Macromolecular Crystallography Krios I-Titan Krios I at Diamond	An allosteric transport mechanism for the AcrAB-TolC Multidrug Efflux Pump Zhao Wang , Guizhen Fan , Corey F Hryc , James N. Blaza , Irina I. Serysheva , Michael F Schmid , Wah Chiu , Ben Luisi , Dijun Du Elife 6 DOI: 10.7554/eLife.24905 Diamond Proposal Number(s): [14043] Open Access Show Abstract ▼ Abstract: Bacterial efflux pumps confer multidrug resistance by transporting diverse antibiotics from the cell. In Gram-negative bacteria, some of these pumps form multi-protein assemblies that span the cell envelope. Here we report the near-atomic resolution cryoEM structures of the Escherichia coli AcrAB-TolC multidrug efflux pump in resting and drug transport states, revealing a quaternary structural switch that allosterically couples and synchronizes initial ligand binding with channel opening. Within the transport-activated state, the channel remains open even though the pump cycles through three distinct conformations. Collectively, our data provide a dynamic mechanism for the assembly and operation of the AcrAB-TolC pump.	Mar 2017
B24-Cryo Soft X-ray Tomography	SuRVoS: Super-Region Volume Segmentation workbench Imanol Luengo , Michele C. Darrow , Matthew C. Spink , Ying Sun , Wei Dai , Cynthia Y. He , Wah Chiu , Tony Pridmore , Alun W. Ashton , Elizabeth M. H. Duke , Mark Basham , Andrew P. French Journal Of Structural Biology DOI: 10.1016/j.jsb.2017.02.007 Open Access Show Abstract ▼ Abstract: Segmentation of biological volumes is a crucial step needed to fully analyse their scientific content. Not having access to convenient tools with which to segment or annotate the data means many biological volumes remain under-utilised. Automatic segmentation of biological volumes is still a very challenging research field, and current methods usually require a large amount of manually-produced training data to deliver a high-quality segmentation. However, the complex appearance of cellular features and the high variance from one sample to another, along with the time-consuming work of manually labelling complete volumes, makes the required training data very scarce or non-existent. Thus, fully automatic approaches are often infeasible for many practical applications. With the aim of unifying the segmentation power of automatic approaches with the user expertise and ability to manually annotate biological samples, we present a new workbench named SuRVoS (Super-Region Volume Segmentation). Within this software, a volume to be segmented is first partitioned into hierarchical segmentation layers (named Super-Regions) and is then interactively segmented with the user's knowledge input in the form of training annotations. SuRVoS first learns from and then extends user inputs to the rest of the volume, while using super-regions for quicker and easier segmentation than when using a voxel grid. These benefits are especially noticeable on noisy, low-dose, biological datasets.	Feb 2017
	A 3D cellular context for the macromolecular world Ardan Patwardhan , Alun Ashton , Robert Brandt , Sarah Butcher , Raffaella Carzaniga , Wah Chiu , Lucy Collinson , Pascal Doux , Elizabeth Duke , Mark H. Ellisman , Erik Franken , Kay Grunewald , Jean-Karim Heriche , Abraham Koster , Werner Kühlbrandt , Ingvar Lagerstedt , Carolyn Larabell , Catherine L. Lawson , Helen Saibil , Eduardo Sanz-García , Sriram Subramaniam , Paul Verkade , Jason R Swedlow , Gerard J Kleywegt Nature Structural & Molecular Biology 21, 841 - 845 DOI: 10.1038/nsmb.2897 PMID: 25289590 Open Access Show Abstract ▼ Abstract: We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community.	Oct 2014
I04-1-Macromolecular Crystallography (fixed wavelength) I24-Microfocus Macromolecular Crystallography	Structure of the AcrAB-TolC multidrug efflux pump Dijun Du , Zhao Wang , Nathan R. James , Jarrod E. Voss , Ewa Klimont , Thelma Ohene-Agyei , Henrietta Venter , Wah Chiu , Ben F. Luisi Nature 509 (7501), 512 - 515 DOI: 10.1038/nature13205 PMID: 24747401 Diamond Proposal Number(s): [9537] Show Abstract ▼ Abstract: The capacity of numerous bacterial species to tolerate antibiotics and other toxic compounds arises in part from the activity of energy-dependent transporters. In Gram-negative bacteria, many of these transporters form multicomponent ‘pumps’ that span both inner and outer membranes and are driven energetically by a primary or secondary transporter component1,2,3,4,5,6,7. A model system for such a pump is the acridine resistance complex of Escherichia coli1. This pump assembly comprises the outer-membrane channel TolC, the secondary transporter AcrB located in the inner membrane, and the periplasmic AcrA, which bridges these two integral membrane proteins. The AcrAB–TolC efflux pump is able to transport vectorially a diverse array of compounds with little chemical similarity, thus conferring resistance to a broad spectrum of antibiotics. Homologous complexes are found in many Gram-negative species, including in animal and plant pathogens. Crystal structures are available for the individual components of the pump2,3,4,5,6,7 and have provided insights into substrate recognition, energy coupling and the transduction of conformational changes associated with the transport process. However, how the subunits are organized in the pump, their stoichiometry and the details of their interactions are not known. Here we present the pseudo-atomic structure of a complete multidrug efflux pump in complex with a modulatory protein partner8 from E. coli. The model defines the quaternary organization of the pump, identifies key domain interactions, and suggests a cooperative process for channel assembly and opening. These findings illuminate the basis for drug resistance in numerous pathogenic bacterial species.	May 2014

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