Real-space refinement in PHENIX for cryo-EM and crystallography.
Pavel V. Afonine,Pavel V. Afonine,Billy K. Poon,Randy J. Read,Oleg V. Sobolev,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Paul D. Adams,Paul D. Adams +9 more
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In this article, the authors describe the implementation of real-space refinement in the phenixreal_space-refine program from the PHENIX suite, which makes use of extra information such as secondary-structure and rotamer-specific restraints.Abstract:
This article describes the implementation of real-space refinement in the phenixreal_space_refine program from the PHENIX suite The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available In addition to standard restraints on covalent geometry, phenixreal_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 A or better shows significant improvement of the models and of the fit of these models to the target mapsread more
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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
Dorothee Liebschner,Pavel V. Afonine,Matthew L. Baker,Gábor Bunkóczi,Vincent B. Chen,Tristan I. Croll,Bradley J. Hintze,Li-Wei Hung,Swati Jain,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Billy K. Poon,Michael G. Prisant,Randy J. Read,Jane S. Richardson,David S. Richardson,Sammito,Oleg V. Sobolev,Duncan H. Stockwell,Thomas C. Terwilliger,Alexandre Urzhumtsev,Alexandre Urzhumtsev,Lizbeth L. Videau,Carmen J. Williams,Paul D. Adams,Paul D. Adams +26 more
TL;DR: Recent developments in the Phenix software package are described in the context of macromolecular structure determination using X-rays, neutrons and electrons.
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The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications.
Ahmad Abdelzaher Zaki Khalifa,Muneyoshi Ichikawa,Daniel Dai,Shintaroh Kubo,Shintaroh Kubo,Corbin Black,Katya Peri,Thomas S. McAlear,Simon Veyron,Shun Kai Yang,Javier Vargas,Susanne Bechstedt,Jean-François Trempe,Khanh Huy Bui +13 more
TL;DR: The structural study of the doublets of Chlamydomonas reinhardtii and Tetrahymena thermophila shows that the inner junction serves as an interaction hub that involves tubulin post-translational modifications that contribute to the stability of thedoublet and hence, normal ciliary motility.
Journal ArticleDOI
Structures and distributions of SARS-CoV-2 spike proteins on intact virions.
Zunlong Ke,Joaquín Otón,Kun Qu,Mirko Cortese,Vojtech Zila,Lesley McKeane,Takanori Nakane,Jasenko Zivanov,Christopher J. Neufeldt,Berati Cerikan,John M. Lu,Julia Peukes,Xiaoli Xiong,Hans-Georg Kräusslich,Sjors H.W. Scheres,Ralf Bartenschlager,Ralf Bartenschlager,John A. G. Briggs +17 more
TL;DR: Cryo-electron microscopy and tomography is applied to image intact SARS-CoV-2 virions, determining the high-resolution structure, conformational flexibility and distribution of S trimers in situ on the virion surface and providing a basis from which to understand interactions between S and neutralizing antibodies during infection or vaccination.
Journal ArticleDOI
Structure of replicating SARS-CoV-2 polymerase.
Hauke S. Hillen,Goran Kokic,Lucas Farnung,Christian Dienemann,Dimitry Tegunov,Patrick Cramer +5 more
TL;DR: A cryo-electron microscopy structure of the RNA-dependent RNA polymerase of SARS-CoV-2 sheds light on coronavirus replication and enables the analysis of the inhibitory mechanisms of candidate antiviral drugs.
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Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies.
Daniel Wrapp,Dorien De Vlieger,Kizzmekia S. Corbett,Gretel M. Torres,Nianshuang Wang,Wander Van Breedam,Kenny Roose,Loes van Schie,Markus Hoffmann,Stefan Pöhlmann,Barney S. Graham,Nico Callewaert,Bert Schepens,Xavier Saelens,Jason S. McLellan +14 more
TL;DR: The isolation of single-domain antibodies (VHHs) from a llama immunized with prefusion-stabilized coronavirus spikes provide a molecular basis for the neutralization of pathogenic betacoronaviruses by VHHs and suggest that these molecules may serve as useful therapeutics during coronav virus outbreaks.
References
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The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
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Coot: model-building tools for molecular graphics.
Paul Emsley,Kevin Cowtan +1 more
TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
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Features and development of Coot.
TL;DR: Coot is a molecular-graphics program designed to assist in the building of protein and other macromolecular models and the current state of development and available features are presented.
Journal ArticleDOI
Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
Axel T. Brunger,Axel T. Brunger,Paul D. Adams,G M Clore,W. L. DeLano,Piet Gros,R.W. Grosse-Kunstleve,R.W. Grosse-Kunstleve,Jiansheng Jiang,J. Kuszewski,Michael Nilges,Navraj S. Pannu,Randy J. Read,Luke M. Rice,Thomas Simonson,Gregory L. Warren +15 more
TL;DR: The Crystallography & NMR System (CNS) as mentioned in this paper is a software suite for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy.
Journal ArticleDOI
Improved methods for building protein models in electron density maps and the location of errors in these models.
TL;DR: In this paper, the authors describe strategies and tools that help to alleviate this problem and simplify the model-building process, quantify the goodness of fit of the model on a per-residue basis and locate possible errors in peptide and side-chain conformations.