Abstract
MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (<xref ref-type="bibr" rid="bib26">Shi et al., 2013</xref>). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination.
Authors
5
- Brent L Nannenga (first)
- Dan Shi (additional)
- Johan Hattne (additional)
- Francis E Reyes (additional)
- Tamir Gonen (additional)
References
32
Referenced
112
10.1107/S0907444909052925
/ Acta Crystallographica Section D, Biological Crystallography / PHENIX: a comprehensive Python-based system for macromolecular structure solution by Adams (2010)10.1016/J.Jsb.2009.11.014
/ Journal of Structural Biology / The resolution dependence of optimal exposures in liquid nitrogen temperature electron cryomicroscopy of catalase crystals by Baker (2010)10.1107/S0907444910048675
/ Acta Crystallographica Section D, Biological Crystallography / iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM by Battye (2011)10.1107/S0907444904016427
/ Acta Crystallographica Section D, Biological Crystallography / Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT by Blanc (2004)10.1107/S0907444909042073
/ Acta Crystallographica Section D, Biological Crystallography / MolProbity: all-atom structure validation for macromolecular crystallography by Chen (2010)10.1107/S0907444906022116
/ Acta Crystallographica Section D, Biological Crystallography / The Buccaneer software for automated model building. 1. Tracing protein chains by Cowtan (2006)10.1107/S0567739475000423
/ Acta Crystallographica Section D, Biological Crystallography / Electron-diffraction from single, fully-hydrated, ox liver catalase microcrystals by Dorset (1975a)10.1107/S0021889875009430
/ Journal of Applied Crystallography / Thickness measurements of wet protein crystals in electron-microscope by Dorset (1975b)10.1107/S0907444910007493
/ Acta Crystallographica Section D, Biological Crystallography / Features and development of Coot by Emsley (2010)10.1107/S0907444905036693
/ Acta Crystallographica Section D, Biological Crystallography / Scaling and assessment of data quality by Evans (2006)10.1107/S090744491003982x
/ Acta Crystallographica Section D, Biological Crystallography / An introduction to data reduction: space-group determination, scaling and intensity statistics by Evans (2011)10.1107/S0907444913000061
/ Acta Crystallographica Section D, Biological Crystallography / How good are my data and what is the resolution? by Evans (2013)10.1073/pnas.82.6.1604
/ Proceedings of the National Academy of Sciences of USA / The NADPH binding site on beef liver catalase by Fita (1985)10.1021/Cg101518f
/ Crystal Growth and Design / Polymer-induced heteronucleation for protein single crystal growth: structural elucidation of bovine liver catalase and concanavalin a forms by Foroughi (2011)10.1016/0304-3991(89)90021-1
/ Ultramicroscopy / 3-Dimensional reconstructions from incomplete data - interpretability of density maps at atomic resolution by Glaeser (1989)10.1007/978-1-62703-176-9_9
/ Methods in Molecular Biology / The collection of high-resolution electron diffraction data by Gonen (2013)10.1073/pnas.81.14.4343
/ Proceedings of the National Academy of Sciences of USA / Catalase: a tetrameric enzyme with four tightly bound molecules of NADPH by Kirkman (1984)10.1107/S0907444999007052
/ Acta Crystallographica Section D, Biological Crystallography / Structure of orthorhombic crystals of beef liver catalase by Ko (1999)10.1007/978-1-4020-6316-9_4
/ NATO Science Series II: Mathematics, Physics and Chemistry / Processing diffraction data with MOSFLM by Leslie (2007)10.1016/S0022-2836(67)80042-1
/ Journal of Molecular Biology / Crystal structure of bovine liver catalase - a combined study by x-ray diffraction and electron microscopy by Longley (1967)10.1126/Science.177.4045.268
/ Science / Electron-diffraction of wet proteins - catalase by Matricardi (1972)10.1107/S0907444996012255
/ Acta Crystallographica Section D, Biological Crystallography / Refinement of macromolecular structures by the maximum-likelihood method by Murshudov (1997)10.1038/nmeth.3043
/ Nature Methods / High-resolution structure determination by continuous-rotation data collection in MicroED by Nannenga (2014)10.1002/jcc.20084
/ Journal of Computational Chemistry / UCSF Chimera–a visualization system for exploratory research and analysis by Pettersen (2004)10.1021/bi200130r
/ Biochemistry / Interaction of nitric oxide with catalase: structural and kinetic analysis by Purwar (2011)10.7554/eLife.01345
/ eLife / Three-dimensional electron crystallography of protein microcrystals by Shi (2013)10.1016/S0021-9258(18)74274-9
/ The Journal of Biological Chemistry / Crystalline catalase by Sumner (1937)10.1107/S0907444906046233
/ Acta Crystallographica Section D, Biological Crystallography / Ligand identification using electron-density map correlations by Terwilliger (2007)10.1107/S0907444906017161
/ Acta Crystallographica Section D, Biological Crystallography / Automated ligand fitting by core-fragment fitting and extension into density by Terwilliger (2006)10.1016/S0022-2836(75)80111-2
/ Journal of Molecular Biology / Beef liver catalase structure: interpretation of electron micrographs by Unwin (1975)10.1016/0022-2836(75)90212-0
/ Journal of Molecular Biology / Molecular structure determination by electron microscopy of unstained crystalline specimens by Unwin (1975)10.1107/S0021889897006766
/ Journal of Applied Crystallography / MOLREP: an automated program for molecular replacement by Vagin (1997)
Dates
Type | When |
---|---|
Created | 10 years, 10 months ago (Oct. 10, 2014, 5:30 a.m.) |
Deposited | 1 year, 10 months ago (Oct. 11, 2023, 8:47 p.m.) |
Indexed | 3 weeks, 1 day ago (July 30, 2025, 1:08 p.m.) |
Issued | 10 years, 10 months ago (Oct. 10, 2014) |
Published | 10 years, 10 months ago (Oct. 10, 2014) |
Published Online | 10 years, 10 months ago (Oct. 10, 2014) |
Funders
2
Howard Hughes Medical Institute
10.13039/100000011
Region: Americas
pri (Research institutes and centers)
Labels
2
- Howard Hughes Medical Institute Inc
- HHMI
Howard Hughes Medical Institute
10.13039/100000011
Region: Americas
pri (Research institutes and centers)
Labels
2
- Howard Hughes Medical Institute Inc
- HHMI
@article{Nannenga_2014, title={Structure of catalase determined by MicroED}, volume={3}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/elife.03600}, DOI={10.7554/elife.03600}, journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Nannenga, Brent L and Shi, Dan and Hattne, Johan and Reyes, Francis E and Gonen, Tamir}, year={2014}, month=oct }