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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Recognition of UbcH5c and the nucleosome by the Bmi1/Ring1b ubiquitin ligase complex.
TL;DR: The results point to a novel mechanism of substrate recognition, and control of product formation, by Bmi1/Ring1b, a critical component of PRC1 that heterodimerize via their N‐terminal RING domains to form an active E3 ubiquitin ligase.
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Inhibitors that stabilize a closed RAF kinase domain conformation induce dimerization.
Hugo Lavoie,Neroshan Thevakumaran,Neroshan Thevakumaran,Gwenaëlle Gavory,John J. Li,John J. Li,Abbas Padeganeh,Sébastien Guiral,Jean Duchaine,Daniel Y.L. Mao,Daniel Y.L. Mao,Michel Bouvier,Frank Sicheri,Frank Sicheri,Marc Therrien +14 more
TL;DR: BRET-based biosensors for the extended RAF family are described, suggesting a model whereby ATP-competitive inhibitors mediate RAF dimerization by stabilizing a rigid closed conformation of the kinase domain.
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Full-Length P2X7 Structures Reveal How Palmitoylation Prevents Channel Desensitization
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Cryo-EM structures capture the transport cycle of the P4-ATPase flippase.
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Structure of the intact 14-subunit human cytochrome c oxidase.
TL;DR: It is proposed that the intact complex-IV is a monomer containing 14 subunits, similar to that of the supercomplex I1III2IV1, which was previously assumed as a subunit of complex-I.
References
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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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