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Solving a new R2lox protein structure by microcrystal electron diffraction
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).ORCID iD: 0000-0002-5466-6508
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
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Number of Authors: 72019 (English)In: Science Advances, E-ISSN 2375-2548, Vol. 5, no 8, article id eaax4621Article in journal (Refereed) Published
Abstract [en]

Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure-an R2lox enzyme-solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-angstrom resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.

Place, publisher, year, edition, pages
2019. Vol. 5, no 8, article id eaax4621
National Category
Physical Sciences Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-173201DOI: 10.1126/sciadv.aax4621ISI: 000481798400057PubMedID: 31457106OAI: oai:DiVA.org:su-173201DiVA, id: diva2:1351756
Available from: 2019-09-16 Created: 2019-09-16 Last updated: 2022-03-23Bibliographically approved
In thesis
1. Push the limitations of crystal structure determination by 3D electron diffraction: From inorganic porous materials to biomolecules
Open this publication in new window or tab >>Push the limitations of crystal structure determination by 3D electron diffraction: From inorganic porous materials to biomolecules
2021 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Structure elucidation is fundamental to understanding the chemical and physical properties of a material. Three-dimensional electron diffraction (3D ED) has shown great power for structure determination of nanometer- or submicrometer-sized crystals that are either too small or too complex for X-ray diffraction. 3D ED can be applied to a wide range of crystalline materials from inorganic materials, small organic molecules, to macromolecules. In this thesis, continuous rotation electron diffraction (cRED), also known as micro-crystal electron diffraction (MicroED) in macromolecular crystallography, has been applied for the determination of interesting novel crystal structures. New methods and protocols have been developed to push the current limitations of crystal structure determination by 3D ED.

The structure of silicate zeolite PST-24 is highly disordered. A combination of cRED with high-resolution transmission electron microscopy (HRTEM) revealed its unique channel system with varying dimensionality from 2D to 3D. The aluminum metal-organic framework CAU-23 nanocrystals form aggregates and are very beam sensitive. Its structure, as determined by cRED, is built by twisted helical Al-O chains connected by TDC2- linkers, forming a chiral structure with square channels. The unique structure of CAU-23 provides high stability and high water adsorption capacity, making it an ideal material for ultra-low temperature adsorption driven chillers.

A simple pressure-assisted specimen preparation method, denoted Preassis, has been developed to overcome the challenges in the application of MicroED on biological samples with high viscosity and low crystal concentration. It has been successfully applied for the specimen preparation of several bio-molecular crystals including a novel R2lox metalloenzyme, which was crucial for its structure determination. Furthermore, an investigation of the influence of radiation damage on lysozyme crystals was performed to improve the data quality and final structural model. Finally, the crystal structure of acetylated amyloid-β fragment Ac-Aβ16-20, related to Alzheimer’s disease, has been studied. The crystal has an active optical wave-guiding property with an excitation wavenumber of 488 nm due to its unique packing of Ac-KLVFF β–sheets.

Place, publisher, year, edition, pages
Stockholm: Department of Materials and Environmental Chemistry (MMK), Stockholm University, 2021. p. 82
Keywords
electron crystallography, 3D electron diffraction, cryo-EM specimen preparation, structure determination, porous materials, biomolecules
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-192517 (URN)978-91-7911-448-0 (ISBN)978-91-7911-449-7 (ISBN)
Public defence
2021-06-11, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 09:00 (English)
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Available from: 2021-05-19 Created: 2021-04-22 Last updated: 2022-02-25Bibliographically approved

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Xu, HongyiLebrette, HugoClabbers, Max T. B.Zhao, JingjingGriese, Julia J.Zou, XiaodongHögbom, Martin

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