Three-dimensional electron crystallography of protein microcrystals

We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1–1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name ‘MicroED’, that may have wide applicability in structural biology. DOI: http://dx.doi.org/10.7554/eLife.01345.001

[1]  K. Tani,et al.  Mechanism of aquaporin-4's fast and highly selective water conduction and proton exclusion. , 2009, Journal of molecular biology.

[2]  R. Henderson The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules , 1995, Quarterly Reviews of Biophysics.

[3]  R. Henderson,et al.  Molecular structure determination by electron microscopy of unstained crystalline specimens. , 1975, Journal of molecular biology.

[4]  Yoshinori Fujiyoshi,et al.  Atomic model of plant light-harvesting complex by electron crystallography , 1994, Nature.

[5]  W. Chiu Electron microscopy of frozen, hydrated biological specimens. , 1986, Annual review of biophysics and biophysical chemistry.

[6]  J. Drenth Principles of protein x-ray crystallography , 1994 .

[7]  C. Bugg,et al.  Structure of calmodulin refined at 2.2 A resolution. , 1988, Journal of molecular biology.

[8]  Akinori Kidera,et al.  Surface of bacteriorhodopsin revealed by high-resolution electron crystallography , 1997, Nature.

[9]  M. Shatsky,et al.  A method for the alignment of heterogeneous macromolecules from electron microscopy. , 2009, Journal of structural biology.

[10]  T. Gonen,et al.  Fragment-based phase extension for three-dimensional structure determination of membrane proteins by electron crystallography. , 2011, Structure.

[11]  R. Glaeser,et al.  Limitations to significant information in biological electron microscopy as a result of radiation damage. , 1971, Journal of ultrastructure research.

[12]  T. Gonen The collection of high-resolution electron diffraction data. , 2013, Methods in molecular biology.

[13]  Henning Stahlberg,et al.  Automatic recovery of missing amplitudes and phases in tilt-limited electron crystallography of two-dimensional crystals. , 2011, Physical review. E, Statistical, nonlinear, and soft matter physics.

[14]  D. F. Koenig,et al.  Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution. , 1965, Nature.

[15]  R. Henderson,et al.  Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. , 1990, Journal of molecular biology.

[16]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[17]  A. Schenk Structure determination of membrane proteins by electron crystallography , 2007 .

[18]  T. Amano,et al.  Structure of Lysozyme , 1965 .

[19]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[20]  Gebhard F. X. Schertler,et al.  Protein crystallography with a micrometre-sized synchrotron-radiation beam , 2008, Acta crystallographica. Section D, Biological crystallography.

[21]  Andrew G. W. Leslie,et al.  Processing diffraction data with mosflm , 2007 .

[22]  Jan Pieter Abrahams,et al.  A Medipix quantum area detector allows rotation electron diffraction data collection from submicrometre three-dimensional protein crystals , 2013, Acta crystallographica. Section D, Biological crystallography.

[23]  John E. Johnson,et al.  Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy. , 1995, Structure.

[24]  J. Abrahams,et al.  Image Processing and Lattice Determination for Three-Dimensional Nanocrystals , 2011, Microscopy and Microanalysis.

[25]  Georg Weidenspointner,et al.  Femtosecond X-ray protein nanocrystallography , 2011, Nature.

[26]  Garth J. Williams,et al.  High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography , 2012, Science.

[27]  R Diamond,et al.  Real-space refinement of the structure of hen egg-white lysozyme. , 1977, Journal of molecular biology.

[28]  M. Weiss,et al.  STRUCTURE OF HEN EGG-WHITE LYSOZYME , 2000 .

[29]  S. Harrison,et al.  Lipid–protein interactions in double-layered two-dimensional AQP0 crystals , 2005, Nature.

[30]  S. Kim,et al.  Three-dimensional reconstructions from incomplete data: interpretability of density maps at "atomic" resolution. , 1989, Ultramicroscopy.

[31]  R Henderson,et al.  Electron-crystallographic refinement of the structure of bacteriorhodopsin. , 1996, Journal of molecular biology.

[32]  T. Gonen,et al.  Advances in structural and functional analysis of membrane proteins by electron crystallography. , 2011, Structure.

[33]  R. Henderson,et al.  Three-dimensional model of purple membrane obtained by electron microscopy , 1975, Nature.

[34]  C. Gilmore,et al.  Structure model for the phase AlmFe derived from three-dimensional electron diffraction intensity data collected by a precession technique. Comparison with convergent-beam diffraction , 1998 .

[35]  D. Stokes,et al.  Three-dimensional crystals of Ca2+-ATPase from sarcoplasmic reticulum: merging electron diffraction tilt series and imaging the (h, k, 0) projection. , 1998, Journal of molecular biology.

[36]  B. Matthews,et al.  Structure of bacteriophage T4 lysozyme refined at 1.7 A resolution. , 1987, Journal of molecular biology.

[37]  R Giegé,et al.  Structure of tetragonal hen egg-white lysozyme at 0.94 A from crystals grown by the counter-diffusion method. , 2001, Acta crystallographica. Section D, Biological crystallography.

[38]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[39]  E. Procko,et al.  Distinct properties of Ca2+–calmodulin binding to N- and C-terminal regulatory regions of the TRPV1 channel , 2012, The Journal of general physiology.

[40]  D. Oesterhelt,et al.  Directed manipulation of a flavoprotein photocycle. , 2013, Angewandte Chemie.

[41]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[42]  A. North,et al.  Structure Of Lysozyme: A Fourier Map of the Electron Density at 6 Å Resolution obtained by X-ray Diffraction , 1962, Nature.

[43]  Y. Xiong From electron microscopy to X-ray crystallography: molecular-replacement case studies , 2007, Acta crystallographica. Section D, Biological crystallography.

[44]  Ko Ohno ON THE STRUCTURE OF LYSOZYME , 1954 .

[45]  Florent Cipriani,et al.  CrystalDirect: a new method for automated crystal harvesting based on laser-induced photoablation of thin films. , 2012, Acta crystallographica. Section D, Biological crystallography.

[46]  David Eisenberg,et al.  Crystal structures of truncated alphaA and alphaB crystallins reveal structural mechanisms of polydispersity important for eye lens function , 2010, Protein science : a publication of the Protein Society.

[47]  John L Rubinstein,et al.  The resolution dependence of optimal exposures in liquid nitrogen temperature electron cryomicroscopy of catalase crystals. , 2010, Journal of structural biology.

[48]  E. Dodson Using electron-microscopy images as a model for molecular replacement. , 2001, Acta crystallographica. Section D, Biological crystallography.