Electron diffraction

Colliex, C.; Cowley, J. M.; Dudarev, S. L.; Fink, M.; Gjønnes, J.; Hilderbrandt, R. L.; Howie, A.; Lynch, D. F.; Peng, Lihong; Ren, Gang; Ross, A. W.; Smith, Vernon; Spence, John C. H.; Steeds, J. W.; Wang, J.; Whelan, M. J.; Zvyagin, B. B.

doi:10.1107/97809553602060000593

Cited by 29 publications

(31 citation statements)

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“…Phases for the BVMbound and drug-free MicroED reflections were determined by molecular replacement with Phaser (42) using the X-ray structure of hexameric CTD-SP1 (PDB 5I4T) as the search model. Cycles of real-space and reciprocal space refinements were performed with Coot (43) and phenix.refine (44), using electron scattering factors (45). Torsion angle noncrystallographic symmetry (NCS) restraints were used in the early rounds of refinement.…”

Section: Methodsmentioning

confidence: 99%

MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat

Purdy

Shi

Chrustowicz

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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HIV-1 protease (PR) cleavage of the Gag polyprotein triggers the assembly of mature, infectious particles. Final cleavage of Gag occurs at the junction helix between the capsid protein CA and the SP1 spacer peptide. Here we used MicroED to delineate the binding interactions of the maturation inhibitor bevirimat (BVM) using very thin frozen-hydrated, 3D microcrystals of a CTD-SP1 Gag construct with and without bound BVM. The 2.9-Å MicroED structure revealed that a single BVM molecule stabilizes the six-helix bundle via both electrostatic interactions with the dimethylsuccinyl moiety and hydrophobic interactions with the pentacyclic triterpenoid ring. These results provide insight into the mechanism of action of BVM and related maturation inhibitors that will inform further drug discovery efforts. This study also demonstrates the capabilities of MicroED for structure-based drug design.

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Section: Methodsmentioning

confidence: 99%

MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat

Purdy

Shi

Chrustowicz

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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“…The high image contrast, in both cases, is due to the fact that the heavy-metal ions scatter more electrons compared with the lighter atoms in the sample. [164–166] The heavy-metal coating on the sample permits a high dose with high contrast for easier determination of particle orientation in 3D reconstructions. [167] Negative-staining reagents include phosphotungstic acid salts, ammonium molybdate, uranyl acetate, uranyl formate, and methylamine vanadate.…”

Section: Advances In Et For Soft-materials and Biomaterials Researchmentioning

confidence: 99%

Electron Tomography: A Three‐Dimensional Analytic Tool for Hard and Soft Materials Research

et al. 2015

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Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is a technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. This review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated.

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“…Phases for the BVM-bound and drug-free MicroED reflections were determined by molecular replacement with Phaser 30 using the X-ray structure of hexameric CTD-SP1 (PDB 5I4T) as the search model. Cycles of real space and reciprocal space refinements were performed with Coot 31 and phenix.refine, using electron scattering factors 32 . Torsion-angle NCS restraints were used in the early rounds of refinement.…”

Section: Crystallization Of Ctd-sp1 and Ctd-sp1-bvm The Conditions Fmentioning

confidence: 99%

MicroED Structures of HIV-1 Gag CTD-SP1 Reveal Binding Interactions with the Maturation Inhibitor Bevirimat

Purdy

Shi

Chrustowicz

et al. 2017

Preprint

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Electron diffraction

Cited by 29 publications

References 0 publications

MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat

MicroED structures of HIV-1 Gag CTD-SP1 reveal binding interactions with the maturation inhibitor bevirimat

Electron Tomography: A Three‐Dimensional Analytic Tool for Hard and Soft Materials Research

MicroED Structures of HIV-1 Gag CTD-SP1 Reveal Binding Interactions with the Maturation Inhibitor Bevirimat

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