Literature DB >> 20888960

Fourier-Bessel reconstruction of helical assemblies.

Ruben Diaz1, William J Rice, David L Stokes.   

Abstract

Helical symmetry is commonly used for building macromolecular assemblies. Helical symmetry is naturally present in viruses and cytoskeletal filaments and also occurs during crystallization of isolated proteins, such as Ca-ATPase and the nicotinic acetyl choline receptor. Structure determination of helical assemblies by electron microscopy has a long history dating back to the original work on three-dimensional (3D) reconstruction. A helix offers distinct advantages for structure determination. Not only can one improve resolution by averaging across the constituent subunits, but each helical assembly provides multiple views of these subunits and thus provides a complete 3D data set. This review focuses on Fourier methods of helical reconstruction, covering the theoretical background, a step-by-step guide to the process, and a practical example based on previous work with Ca-ATPase. Given recent results from helical reconstructions at atomic resolution and the development of graphical user interfaces to aid in the process, these methods are likely to continue to make an important contribution to the field of structural biology.
Copyright © 2010 Elsevier Inc. All rights reserved.

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Year:  2010        PMID: 20888960      PMCID: PMC3128834          DOI: 10.1016/S0076-6879(10)82005-1

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN: 0076-6879            Impact factor:   1.600


  51 in total

1.  Locating phospholamban in co-crystals with Ca(2+)-ATPase by cryoelectron microscopy.

Authors:  H S Young; L R Jones; D L Stokes
Journal:  Biophys J       Date:  2001-08       Impact factor: 4.033

2.  Averaging data derived from images of helical structures with different symmetries.

Authors:  D DeRosier; D L Stokes; S A Darst
Journal:  J Mol Biol       Date:  1999-05-28       Impact factor: 5.469

3.  Accurate determination of local defocus and specimen tilt in electron microscopy.

Authors:  Joseph A Mindell; Nikolaus Grigorieff
Journal:  J Struct Biol       Date:  2003-06       Impact factor: 2.867

4.  Do the utrophin tandem calponin homology domains bind F-actin in a compact or extended conformation?

Authors:  Vitold E Galkin; Albina Orlova; Margaret S VanLoock; Edward H Egelman
Journal:  J Mol Biol       Date:  2003-08-29       Impact factor: 5.469

5.  Structure of the calcium pump from sarcoplasmic reticulum at 8-A resolution.

Authors:  P Zhang; C Toyoshima; K Yonekura; N M Green; D L Stokes
Journal:  Nature       Date:  1998-04-23       Impact factor: 49.962

6.  PHOELIX: a package for semi-automated helical reconstruction.

Authors:  M Whittaker; B O Carragher; R A Milligan
Journal:  Ultramicroscopy       Date:  1995-06       Impact factor: 2.689

7.  Three-dimensional cryo-electron microscopy of the calcium ion pump in the sarcoplasmic reticulum membrane.

Authors:  C Toyoshima; H Sasabe; D L Stokes
Journal:  Nature       Date:  1993-04-01       Impact factor: 49.962

8.  Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA.

Authors:  X Yu; S A Jacobs; S C West; T Ogawa; E H Egelman
Journal:  Proc Natl Acad Sci U S A       Date:  2001-07-17       Impact factor: 11.205

Review 9.  The structural basis for coupling of Ca2+ transport to ATP hydrolysis by the sarcoplasmic reticulum Ca2+-ATPase.

Authors:  Jesper Vuust Møller; Claus Olesen; Anne-Marie Lund Jensen; Poul Nissen
Journal:  J Bioenerg Biomembr       Date:  2005-12       Impact factor: 3.853

10.  Structural relationships of actin, myosin, and tropomyosin revealed by cryo-electron microscopy.

Authors:  R A Milligan; P F Flicker
Journal:  J Cell Biol       Date:  1987-07       Impact factor: 10.539

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  20 in total

1.  The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking.

Authors:  Gregory S Allen; Chen-Chou Wu; Tim Cardozo; David L Stokes
Journal:  Structure       Date:  2011-08-04       Impact factor: 5.006

2.  Structure of the SLC4 transporter Bor1p in an inward-facing conformation.

Authors:  Nicolas Coudray; Sean L Seyler; Ralph Lasala; Zhening Zhang; Kathy M Clark; Mark E Dumont; Alexis Rohou; Oliver Beckstein; David L Stokes
Journal:  Protein Sci       Date:  2016-10-21       Impact factor: 6.725

3.  Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy.

Authors:  Nicolas Coudray; Salvatore Valvo; Minghui Hu; Ralph Lasala; Changki Kim; Martin Vink; Ming Zhou; Davide Provasi; Marta Filizola; Juoehi Tao; Jia Fang; Pawel A Penczek; Iban Ubarretxena-Belandia; David L Stokes
Journal:  Proc Natl Acad Sci U S A       Date:  2013-01-22       Impact factor: 11.205

4.  X-ray diffraction from nonuniformly stretched helical molecules.

Authors:  Momcilo Prodanovic; Thomas C Irving; Srboljub M Mijailovich
Journal:  J Appl Crystallogr       Date:  2016-04-18       Impact factor: 3.304

5.  Real-space processing of helical filaments in SPARX.

Authors:  Elmar Behrmann; Guozhi Tao; David L Stokes; Edward H Egelman; Stefan Raunser; Pawel A Penczek
Journal:  J Struct Biol       Date:  2012-01-11       Impact factor: 2.867

Review 6.  A helical processing pipeline for EM structure determination of membrane proteins.

Authors:  Lauren S Fisher; Andrew Ward; Ronald A Milligan; Nigel Unwin; Clinton S Potter; Bridget Carragher
Journal:  Methods       Date:  2011-09-20       Impact factor: 3.608

7.  An Ultrastructural Study of the Extruded Polar Tube of Anncaliia algerae (Microsporidia).

Authors:  Peter M Takvorian; Bing Han; Ann Cali; William J Rice; Leslie Gunther; Frank Macaluso; Louis M Weiss
Journal:  J Eukaryot Microbiol       Date:  2019-08-08       Impact factor: 3.346

8.  Surface for catalysis by poliovirus RNA-dependent RNA polymerase.

Authors:  Jing Wang; John M Lyle; Esther Bullitt
Journal:  J Mol Biol       Date:  2013-04-11       Impact factor: 5.469

9.  Deducing the symmetry of helical assemblies: Applications to membrane proteins.

Authors:  Nicolas Coudray; Ralph Lasala; Zhening Zhang; Kathy M Clark; Mark E Dumont; David L Stokes
Journal:  J Struct Biol       Date:  2016-05-30       Impact factor: 2.867

10.  Calcium sensitive ring-like oligomers formed by synaptotagmin.

Authors:  Jing Wang; Oscar Bello; Sarah M Auclair; Jing Wang; Jeff Coleman; Frederic Pincet; Shyam S Krishnakumar; Charles V Sindelar; James E Rothman
Journal:  Proc Natl Acad Sci U S A       Date:  2014-09-08       Impact factor: 11.205

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