<i>PHENIX</i>: a comprehensive Python-based system for macromolecular structure solution

Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, G.; Chen, Vincent B.; Davis, Ian; Echols, Nathaniel; Headd, Jeffrey J.; Hung, Li‐Wei; Kapral, Gary J.; Grosse‐Kunstleve, Ralf W.; McCoy, Airlie J.; Moriarty, Nigel W.; Oeffner, Robert D.; Read, R.J.; Richardson, David C.; Richardson, Jane S.; Terwilliger, Thomas C.; Zwart, Peter H.

doi:10.1107/97809553602060000865

Cited by 5,428 publications

(6,916 citation statements)

References 26 publications

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“…The electron density maps from Phaser showed continuous electron density throughout the model and indicated slight tilting of M5. The model was adjusted accordingly in Coot and refined in Phenix 36,37 . A composite simulated-annealing omit electron density map was constructed using Phenix 36 and this map confirmed that the only discernable difference in the overall structure was the tilting of M5 (Fig.…”

Section: Methodsmentioning

confidence: 99%

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Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT

Diver

Pedi

Koide

et al. 2018

Nature

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The maturation of Ras GTPases, and ~200 other cellular CaaX proteins, involves three enzymatic steps: addition of a farnesyl or geranylgeranyl prenyl lipid to the cysteine (C) in the C-terminal CaaX motif, proteolytic cleavage of the aaX residues, and methylation of the exposed prenylcysteine residue at its terminal carboxylate1. This final step is catalyzed by isoprenylcysteine carboxyl methyltransferase (ICMT), a eukaryotic-specific integral membrane enzyme of the endoplasmic reticulum (ER)2. ICMT is the only cellular enzyme known to methylate prenylcysteine substrates; methylation is important for their biological functions, including the membrane localisations and subsequent activities of Ras1, prelamin A3, and Rab4. ICMT inhibition has potential for combating progeria3 and cancer5–8. Here we present an X-ray structure of ICMT, at 2.3 Å resolution, in complex with its cofactor, an ordered lipid molecule and a monobody inhibitor. The active site spans cytosolic and membrane-exposed regions, indicating distinct entry routes for its cytosolic methyl donor, S-adenosyl-L-methionine (AdoMet), and for prenylcysteine substrates, which are associated with the ER membrane. The structure suggests how ICMT overcomes the topographical challenge and unfavourable energetics of bringing two reactants that have different cellular localisations together in a membrane environment – a relatively uncharacterized, but defining feature of many integral membrane enzymes.

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Section: Methodsmentioning

confidence: 99%

“…e , A composite omit electron density map (2F o -F c , contoured at 1 σ and calculated from 35 – 4.0 Å resolution) for the X-ray structure of ICMT without the monobody. The composite omit maps, which reduce model-bias, were obtained using Phenix 36 .…”

Section: Extended Datamentioning

confidence: 99%

Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT

Diver

Pedi

Koide

et al. 2018

Nature

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“…Initial rigid body fit of an atomic model of the kirromycin-stalled E. coli ribosome complex 58 lacking EF-Tu and Phe-tRNA Phe was performed against the masked cryo-EM map of the GTPase-activated state using Chimera, followed by rigid body refinement of individual chains in PHENIX 68 program. The atomic model of SelB with exception of tandem winged-helix motifs 3 and 4 was obtained by combining manual rebuilding and homology modelling with density-guided energy optimization, as implemented in the Rosetta package 69,70 , employing a template derived from Methanococcus maripaludis SelB (PDB ID: 4AC9) 9 and alignment provided by the HHPRED server 71 .…”

Section: Atomic Model Refinement Pseudo-crystallographic Refinement mentioning

confidence: 99%

The pathway to GTPase activation of elongation factor SelB on the ribosome

Fischer

Neumann

Bock

et al. 2016

Nature

106

137

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“…The structure was solved using SHELX (Sheldrick, 2010) within HKL2MAP (Pape and Schneider, 2004); initial model building was performed using ARP/wARP (Langer et al, 2008). Refinement proceeded with cycles of automated refinement in PHENIX (Adams et al, 2010) and manual rebuilding in COOT (Emsley et al, 2010). Details of the diffraction data and refined models are reported in Supplementary Table SII.…”

Section: Protein Expression and Purification For Crystallizationmentioning

confidence: 99%

A widespread family of bacterial cell wall assembly proteins

et al. 2011

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Teichoic acids and acidic capsular polysaccharides are major anionic cell wall polymers (APs) in many bacteria, with various critical cell functions, including maintenance of cell shape and structural integrity, charge and cation homeostasis, and multiple aspects of pathogenesis. We have identified the widespread LytR-Cps2A-Psr (LCP) protein family, of previously unknown function, as novel enzymes required for AP synthesis. Structural and biochemical analysis of several LCP proteins suggest that they carry out the final step of transferring APs from their lipid-linked precursor to cell wall peptidoglycan (PG). In Bacillus subtilis, LCP proteins are found in association with the MreB cytoskeleton, suggesting that MreB proteins coordinate the insertion of the major polymers, PG and AP, into the cell wall.

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PHENIX: a comprehensive Python-based system for macromolecular structure solution

Cited by 5,428 publications

References 26 publications

Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT

Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT

The pathway to GTPase activation of elongation factor SelB on the ribosome

A widespread family of bacterial cell wall assembly proteins

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