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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Structure of the Human cGAS-DNA Complex Reveals Enhanced Control of Immune Surveillance.
Wen Zhou,Aaron T. Whiteley,Carina C. de Oliveira Mann,B.R. Morehouse,Radosław P. Nowak,Eric S. Fischer,Nathanael S. Gray,John J. Mekalanos,Philip J. Kranzusch +8 more
TL;DR: How DNA-sensing in humans adapted for enhanced specificity is defined and Crystal structures reveal why removal of human substitutions relaxes DNA-length specificity and explain how human-specific DNA interactions favor cGAS oligomerization.
Journal ArticleDOI
Architecture of the large subunit of the mammalian mitochondrial ribosome
Basil J. Greber,Daniel Boehringer,Alexander Leitner,Philipp Bieri,Felix Voigts-Hoffmann,Jan P. Erzberger,Marc Leibundgut,Ruedi Aebersold,Nenad Ban +8 more
TL;DR: The three-dimensional structure of the 39S large subunit of the porcine mitochondrial ribosome determined by cryo-electron microscopy at 4.9 Å resolution is presented and reveals the unique features of the 37S subunit at near-atomic resolution and provides detailed insight into the architecture of the polypeptide exit site.
Journal ArticleDOI
An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser
Michihiro Suga,Michihiro Suga,Fusamichi Akita,Fusamichi Akita,Keitaro Yamashita,Yoshiki Nakajima,Go Ueno,Hongjie Li,Hongjie Li,Takahiro Yamane,Kunio Hirata,Yasufumi Umena,Shinichiro Yonekura,Long Jiang Yu,Hironori Murakami,Takashi Nomura,Tetsunari Kimura,Minoru Kubo,Seiki Baba,Takashi Kumasaka,Kensuke Tono,Makina Yabashi,Hiroshi Isobe,Kizashi Yamaguchi,Masaki Yamamoto,Hideo Ago,Jian Ren Shen +26 more
TL;DR: To reveal the mechanism of water oxidation, structures of PSII in the S1, S2, and S3 states by x-ray free-electron laser serial crystallography reveal details of photosynthetic oxygen evolution.
Journal ArticleDOI
Structure of the human TRPM4 ion channel in a lipid nanodisc
Henriette Elisabeth Autzen,Henriette Elisabeth Autzen,Alexander G. Myasnikov,Melody G. Campbell,Daniel Asarnow,David Julius,Yifan Cheng +6 more
TL;DR: Two structures of full-length human TRPM4 embedded in lipid nanodiscs at ~3-angstrom resolution, as determined by single-particle cryo–electron microscopy reveal a general architecture for this major subfamily of TRP channels and a well-defined calcium-binding site within the intracellular side of the S1-S4 domain.
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MFN1 structures reveal nucleotide-triggered dimerization critical for mitochondrial fusion
Yu-Lu Cao,Shuxia Meng,Yang Chen,Jian-Xiong Feng,Dong-Dong Gu,Bing Yu,Yu-Jie Li,Jinyu Yang,Shuang Liao,David C. Chan,Song Gao +10 more
TL;DR: A mechanistic model for MFN1-mediated mitochondrial tethering is proposed and the results shed light on the molecular basis of mitochondrial fusion and mitofusin-related human neuromuscular disorders.
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
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.