3D reconstruction from 2D crystal image and diffraction data.

Electron crystallography of 2D protein crystals can determine the structure of membrane embedded proteins at high resolution. Images or electron diffraction patterns are recorded with the electron microscope of the frozen hydrated samples, and the 3D structure of the proteins is then determined by computer data processing. Here we introduce the image-processing algorithms for crystallographic Fourier space based methods using the Medical Research Council (MRC) programs, and illustrate the usage of the software packages 2dx, XDP, and IPLT.

[1]  Tamir Gonen,et al.  Aquaporin-0 membrane junctions reveal the structure of a closed water pore , 2004, Nature.

[2]  Henning Stahlberg,et al.  Iplt--image processing library and toolkit for the electron microscopy community. , 2003, Journal of structural biology.

[3]  M F Schmid,et al.  A brief description of I.C.E.: the integrated crystallographic environment. , 1996, Journal of structural biology.

[4]  J. Lepault,et al.  Structure of purple membrane from halobacterium halobium: recording, measurement and evaluation of electron micrographs at 3.5 Å resolution , 1986 .

[5]  Xiangyan Zeng,et al.  2dx_merge: data management and merging for 2D crystal images. , 2007, Journal of structural biology.

[6]  A. Wilson,et al.  Determination of Absolute from Relative X-Ray Intensity Data , 1942, Nature.

[7]  R A Crowther,et al.  MRC image processing programs. , 1996, Journal of structural biology.

[8]  Xiangyan Zeng,et al.  A maximum likelihood approach to two-dimensional crystals. , 2007, Journal of structural biology.

[9]  R Henderson,et al.  An atomic model for the structure of bacteriorhodopsin. , 1990, Biochemical Society transactions.

[10]  Henning Stahlberg,et al.  The 4.5 A structure of human AQP2. , 2005, Journal of molecular biology.

[11]  Catherine Vénien-Bryan,et al.  Two-dimensional Crystallization of Membrane Proteins , 2005 .

[12]  Ben Hankamer,et al.  Symmetry: A guide to its application in 2D electron crystallography. , 2007, Journal of structural biology.

[13]  T. Yeates,et al.  Protein crystals and their evil twins. , 1999, Structure.

[14]  Q. Ramasse,et al.  Application of two-dimensional crystallography and image processing to atomic resolution Z-contrast images. , 2009, Journal of electron microscopy.

[15]  Ansgar Philippsen,et al.  The contrast-imaging function for tilted specimens. , 2007, Ultramicroscopy.

[16]  Xiangyan Zeng,et al.  2dx--user-friendly image processing for 2D crystals. , 2007, Journal of structural biology.

[17]  R Dargahi,et al.  SPECTRA: a system for processing electron images of crystals. , 1993, Ultramicroscopy.

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

[19]  A. Vagin,et al.  MOLREP: an Automated Program for Molecular Replacement , 1997 .

[20]  W. Kühlbrandt,et al.  Molecular architecture of the undecameric rotor of a bacterial Na+-ATP synthase. , 2002, Journal of molecular biology.

[21]  Matthew D. Pagel,et al.  The structure of the prokaryotic cyclic nucleotide-modulated potassium channel MloK1 at 16 A resolution. , 2007, Structure.

[22]  HansenPer Christian The truncated SVD as a method for regularization , 1987 .

[23]  Xiangyan Zeng,et al.  Automatic lattice determination for two-dimensional crystal images. , 2007, Journal of structural biology.

[24]  T. Baker Electron Crystallography of Biological Macromolecules , R. M. Glaeser, K. Downing, D. DeRosier, W. Chiu, J. Frank. Oxford University Press; 2007, 476 pages. ISBN 0195088719 (Hardcover) , 2009, Microscopy and Microanalysis.

[25]  Andreas Engel,et al.  The 5 angstrom structure of heterologously expressed plant aquaporin SoPIP2;1 , 2005 .

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

[27]  Ansgar Philippsen,et al.  Collaborative EM image processing with the IPLT image processing library and toolbox. , 2007, Journal of structural biology.

[28]  K. Downing,et al.  Performance of a 2k CCD camera designed for electron crystallography at 400 kV. , 1999, Ultramicroscopy.

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

[30]  N Grigorieff,et al.  Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 A in ice. , 1998, Journal of molecular biology.

[31]  A. Kidera,et al.  The structure of bacteriorhodopsin at 3.0 A resolution based on electron crystallography: implication of the charge distribution. , 1999, Journal of molecular biology.

[32]  R. Henderson,et al.  Molecular Structure Determination by Electron Microscopy of Unstained Crystalline Specimens , 1989 .

[33]  Kazushi Kimura,et al.  Implications of the aquaporin-4 structure on array formation and cell adhesion. , 2006, Journal of molecular biology.

[34]  Valerio Mariani,et al.  Transfer of tilted sample information in transmission electron microscopy , 2010 .

[35]  R Henderson,et al.  Analysis of electron microscope images and electron diffraction patterns of thin crystals of phi 29 connectors in ice. , 1994, Journal of molecular biology.

[36]  J M Carazo,et al.  XMIPP: a new generation of an open-source image processing package for electron microscopy. , 2004, Journal of structural biology.

[37]  S. H. YÜ,et al.  Determination of Absolute from Relative X-Ray Intensity Data , 1942, Nature.

[38]  Sven Hovmöller,et al.  CRISP: crystallographic image processing on a personal computer , 1992 .

[39]  Andreas Engel,et al.  Structural determinants of water permeation through aquaporin-1 , 2000, Nature.

[40]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[41]  U Aebi,et al.  2D crystallization: from art to science. , 1992, Ultramicroscopy.

[42]  Xiangyan Zeng,et al.  3D reconstruction of 2D crystals , 2011, ACM-SE '11.

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