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
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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
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Cyclic GMP-AMP Containing Mixed Phosphodiester Linkages Is An Endogenous High-Affinity Ligand for STING.
TL;DR: The crystal structure of STING bound to 2'3'-cGAMP revealed the structural basis of this high-affinity binding and a ligand-induced conformational change in STING that may underlie its activation, and showed that endogenous cGAMP in mammalian cells contains two distinct phosphodiester linkages.
Journal ArticleDOI
High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography
Sébastien Boutet,Lukas Lomb,Garth J. Williams,Thomas R. M. Barends,Andrew Aquila,R. Bruce Doak,Uwe Weierstall,Daniel P. DePonte,Jan Steinbrener,Robert L. Shoeman,Marc Messerschmidt,Anton Barty,Thomas A. White,Stephan Kassemeyer,Richard A. Kirian,M. Marvin Seibert,Paul A. Montanez,C.J. Kenney,Ryan Herbst,P. Hart,J. Pines,Gunther Haller,Sol M. Gruner,Hugh T. Philipp,Mark W. Tate,Marianne Hromalik,Lucas J. Koerner,Niels van Bakel,John Morse,W. Ghonsalves,David Arnlund,Michael J. Bogan,Carl Caleman,Raimund Fromme,Christina Y. Hampton,Mark S. Hunter,Linda C. Johansson,Gergely Katona,Christopher Kupitz,Mengning Liang,Andrew V. Martin,Karol Nass,Lars Redecke,Lars Redecke,Francesco Stellato,Nicusor Timneanu,Dingjie Wang,Nadia A. Zatsepin,Donald W. Schafer,James Defever,Richard Neutze,Petra Fromme,John C. H. Spence,Henry N. Chapman,Ilme Schlichting +54 more
TL;DR: Serial femtosecond crystallography (SFX) is applied using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals of the well-characterized model protein lysozyme, demonstrating the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.
Journal ArticleDOI
Cyclic [G(2′,5′)pA(3′,5′)p] Is the Metazoan Second Messenger Produced by DNA-Activated Cyclic GMP-AMP Synthase
Pu Gao,Manuel Ascano,Wu Yang,Winfried Barchet,Barbara L. Gaffney,Thomas Zillinger,Artem A. Serganov,Liu Yizhou,Roger A. Jones,Gunther Hartmann,Thomas Tuschl,Dinshaw J. Patel +11 more
TL;DR: Structural, chemical, biochemical, and cellular assays are combined to demonstrate that this second messenger contains G(2',5')pA and A(3',5']pG phosphodiester linkages, designated c[G(2,5')sDNA binding, cGAS] as a founding member of a family of metazoan 2',5'-containing cyclic heterodinucleotide second messengers distinct from bacterial 3',5' cyclic dinucleotides
Journal ArticleDOI
Structure-Based Design of a Fusion Glycoprotein Vaccine for Respiratory Syncytial Virus
Jason S. McLellan,Man Chen,M. Gordon Joyce,Mallika Sastry,Guillaume Stewart-Jones,Yongping Yang,Baoshan Zhang,Lei Chen,Sanjay Srivatsan,Anqi Zheng,Tongqing Zhou,Kevin W. Graepel,Azad Kumar,Syed M. Moin,Jeffrey C. Boyington,Gwo-Yu Chuang,Cinque Soto,Ulrich Baxa,Arjen Q. Bakker,Hergen Spits,Tim Beaumont,Zizheng Zheng,Ningshao Xia,Sung Youl Ko,John Paul Todd,Srinivas S. Rao,Barney S. Graham,Peter D. Kwong +27 more
TL;DR: A viral antigen is sought that provides greater protection than currently available vaccines and focused on antigenic site Ø, a metastable site specific to the prefusion state of the RSV fusion (F) glycoprotein, as this site is targeted by extremely potent RSV-neutralizing antibodies.
Journal ArticleDOI
Structural basis of Wnt recognition by Frizzled.
TL;DR: The 3.25 angstrom structure of Xenopus Wnt8 (XWnt8) in complex with mouse Frizzled-8 (Fz8) cysteine-rich domain (CRD) reveals an unusual two-domain Wnt structure, resembling a “hand” with “thumb” and “index” fingers extended to grasp the Fz8-CRD at two distinct binding sites.
References
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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
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Journal ArticleDOI
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Airlie J. McCoy,Ralf W. Grosse-Kunstleve,Paul D. Adams,Martyn Winn,Laurent C. Storoni,Randy J. Read +5 more
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