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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
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.
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Jun 2024
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I03-Macromolecular Crystallography
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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
Open Access
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.
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Dec 2021
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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
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.
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May 2021
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Talos-Talos Arctica at Diamond
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Open Access
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.
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Aug 2018
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I24-Microfocus Macromolecular Crystallography
Krios I-Titan Krios I at Diamond
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Diamond Proposal Number(s):
[14043]
Open Access
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.
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Mar 2017
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B24-Cryo Soft X-ray Tomography
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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
Open Access
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.
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Feb 2017
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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
Open Access
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.
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Oct 2014
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I04-1-Macromolecular Crystallography (fixed wavelength)
I24-Microfocus Macromolecular Crystallography
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Diamond Proposal Number(s):
[9537]
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.
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May 2014
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