PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams,Paul D. Adams,Pavel V. Afonine,Gábor Bunkóczi,Vincent B. Chen,Ian W. Davis,Nathaniel Echols,Jeffrey J. Headd,Li-Wei Hung,Gary J. Kapral,Ralf W. Grosse-Kunstleve,Airlie J. McCoy,Nigel W. Moriarty,Robert D. Oeffner,Randy J. Read,David S. Richardson,Jane S. Richardson,Thomas C. Terwilliger,Peter H. Zwart +18 more
Reads0
Chats0
TLDR
The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.Abstract:
Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.read more
Citations
More filters
Journal ArticleDOI
The Pseudokinase MLKL Mediates Necroptosis via a Molecular Switch Mechanism
James M. Murphy,Peter E. Czabotar,Peter E. Czabotar,Joanne M Hildebrand,Joanne M Hildebrand,Isabelle S Lucet,Jian-Guo Zhang,Jian-Guo Zhang,Silvia Alvarez-Diaz,Silvia Alvarez-Diaz,Rowena S. Lewis,Rowena S. Lewis,Najoua Lalaoui,Najoua Lalaoui,Donald Metcalf,Donald Metcalf,Andrew I. Webb,Andrew I. Webb,Samuel N. Young,Samuel N. Young,Leila N. Varghese,Leila N. Varghese,Gillian M. Tannahill,Gillian M. Tannahill,Esme C. Hatchell,Esme C. Hatchell,Ian J. Majewski,Ian J. Majewski,Toru Okamoto,Toru Okamoto,Renwick C. J. Dobson,Renwick C. J. Dobson,Douglas J. Hilton,Douglas J. Hilton,Jeffrey J. Babon,Jeffrey J. Babon,Nicos A. Nicola,Nicos A. Nicola,Andreas Strasser,Andreas Strasser,John Silke,John Silke,Warren S. Alexander,Warren S. Alexander +43 more
TL;DR: Structural-guided mutation of the MLKL pseudoactive site resulted in constitutive, RIPK3-independent necroptosis, demonstrating that modification ofMLKL is essential for propagation of the ne croptosis pathway downstream of RIPK 3.
Journal ArticleDOI
Principles of activation and permeation in an anion-selective Cys-loop receptor.
Ryan E. Hibbs,Eric Gouaux +1 more
TL;DR: The first three-dimensional structure, to the authors' knowledge, of an inhibitory anion-selective Cys-loop receptor, the homopentameric Caenorhabditis elegans glutamate-gated chloride channel α (GluCl), is presented at 3.3 Å resolution.
Journal ArticleDOI
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
Neuropilin-1 is a host factor for SARS-CoV-2 infection.
James L. Daly,Boris Simonetti,Katja Klein,Kai-En Chen,Maia Kavanagh Williamson,Carlos Antón-Plágaro,Deborah K. Shoemark,Lorena Simón-Gracia,Michael Bauer,Reka Hollandi,Urs F. Greber,Peter Horvath,Peter Horvath,Richard B. Sessions,Ari Helenius,Julian A. Hiscox,Julian A. Hiscox,Tambet Teesalu,David A. Matthews,Andrew D. Davidson,Brett M. Collins,Peter J. Cullen,Yohei Yamauchi,Yohei Yamauchi +23 more
TL;DR: It is shown that neuropilin-1 (NRP1), which is known to bind furin-cleaved substrates, potentiates SARS-CoV-2 infectivity and serves as a host factor for Sars-Cov-2 infection and may potentially provide a therapeutic target for COVID-19.
Journal ArticleDOI
Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions
Wei Liu,Eugene Chun,Aaron Thompson,Pavel Chubukov,Fei Xu,Vsevolod Katritch,Gye Won Han,Christopher B. Roth,Laura H. Heitman,Adriaan P. IJzerman,Vadim Cherezov,Raymond C. Stevens +11 more
TL;DR: The high-resolution structure of a stabilized version of the human A2Aadenosine receptor (A2AAR) reveals the position of about 60 internal waters, which suggests an almost continuous channel in the GPCR and can explain the allosteric effects of Na+ on ligand binding and how cholesterol may contribute to G PCR stabilization.
References
More filters
Journal ArticleDOI
A short history of SHELX
TL;DR: This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
Journal ArticleDOI
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.
Journal ArticleDOI
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.
Journal ArticleDOI
Phaser crystallographic software
Airlie J. McCoy,Ralf W. Grosse-Kunstleve,Paul D. Adams,Martyn Winn,Laurent C. Storoni,Randy J. Read +5 more
TL;DR: A description is given of Phaser-2.1: software for phasing macromolecular crystal structures by molecular replacement and single-wavelength anomalous dispersion phasing.