Literature DB >> 18403197

Towards atomic resolution structural determination by single-particle cryo-electron microscopy.

Z Hong Zhou1.   

Abstract

Recent advances in cryo-electron microscopy and single-particle reconstruction (collectively referred to as 'cryoEM') have made it possible to determine the three-dimensional (3D) structures of several macromolecular complexes at near-atomic resolution ( approximately 3.8-4.5A). These achievements were accomplished by overcoming the challenges in sample handling, instrumentation, image processing, and model building. At near-atomic resolution, many detailed structural features can be resolved, such as the turns and deep grooves of helices, strand separation in beta sheets, and densities for loops and bulky amino acid side chains. Such structural data of the cytoplasmic polyhedrosis virus (CPV), the Epsilon 15 bacteriophage and the GroEL complex have provided valuable constraints for atomic model building using integrative tools, thus significantly enhancing the value of the cryoEM structures. The CPV structure revealed a drastic conformational change from a helix to a beta hairpin associated with RNA packaging and replication, coupling of RNA processing and release, and the long sought-after polyhedrin-binding domain. These latest advances in single-particle cryoEM provide exciting opportunities for the 3D structural determination of viruses and macromolecular complexes that are either too large or too heterogeneous to be investigated by conventional X-ray crystallography or nuclear magnetic resonance (NMR) methods.

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Year:  2008        PMID: 18403197      PMCID: PMC2714865          DOI: 10.1016/j.sbi.2008.03.004

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  75 in total

1.  Diversity of functions of proteins with internal symmetry in spatial arrangement of secondary structural elements.

Authors:  K Kinoshita; A Kidera; N Go
Journal:  Protein Sci       Date:  1999-06       Impact factor: 6.725

2.  EMAN: semiautomated software for high-resolution single-particle reconstructions.

Authors:  S J Ludtke; P R Baldwin; W Chiu
Journal:  J Struct Biol       Date:  1999-12-01       Impact factor: 2.867

Review 3.  CCD detectors in high-resolution biological electron microscopy.

Authors:  A R Faruqi; S Subramaniam
Journal:  Q Rev Biophys       Date:  2000-02       Impact factor: 5.318

4.  Topologically linked protein rings in the bacteriophage HK97 capsid.

Authors:  W R Wikoff; L Liljas; R L Duda; H Tsuruta; R W Hendrix; J E Johnson
Journal:  Science       Date:  2000-09-22       Impact factor: 47.728

5.  Crystal structure of the DsbB-DsbA complex reveals a mechanism of disulfide bond generation.

Authors:  Kenji Inaba; Satoshi Murakami; Mamoru Suzuki; Atsushi Nakagawa; Eiki Yamashita; Kengo Okada; Koreaki Ito
Journal:  Cell       Date:  2006-11-17       Impact factor: 41.582

6.  FREALIGN: high-resolution refinement of single particle structures.

Authors:  Nikolaus Grigorieff
Journal:  J Struct Biol       Date:  2006-06-02       Impact factor: 2.867

7.  The atomic structure of the bluetongue virus core.

Authors:  J M Grimes; J N Burroughs; P Gouet; J M Diprose; R Malby; S Ziéntara; P P Mertens; D I Stuart
Journal:  Nature       Date:  1998-10-01       Impact factor: 49.962

8.  Reliability of phases retrieved from 400-kV spot-scan images of purple membranes acquired on a slow-scan CCD camera.

Authors:  M B Sherman; W Chiu
Journal:  J Microsc       Date:  1997-12       Impact factor: 1.758

9.  CTF determination of images of ice-embedded single particles using a graphics interface.

Authors:  Z H Zhou; S Hardt; B Wang; M B Sherman; J Jakana; W Chiu
Journal:  J Struct Biol       Date:  1996 Jan-Feb       Impact factor: 2.867

10.  The correlation averaging of a regularly arranged bacterial cell envelope protein.

Authors:  W O Saxton; W Baumeister
Journal:  J Microsc       Date:  1982-08       Impact factor: 1.758

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  66 in total

1.  EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps.

Authors:  Steffen Lindert; Nathan Alexander; Nils Wötzel; Mert Karakaş; Phoebe L Stewart; Jens Meiler
Journal:  Structure       Date:  2012-03-07       Impact factor: 5.006

2.  Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking.

Authors:  Mariah R Baker; Ian Rees; Steven J Ludtke; Wah Chiu; Matthew L Baker
Journal:  Structure       Date:  2012-03-07       Impact factor: 5.006

3.  Ab initio protein modeling into CryoEM density maps using EM-Fold.

Authors:  Steffen Lindert; Tommy Hofmann; Nils Wötzel; Mert Karakaş; Phoebe L Stewart; Jens Meiler
Journal:  Biopolymers       Date:  2012-02-03       Impact factor: 2.505

4.  Quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy.

Authors:  Hua Li; Junrui Zhang; Richard D Vierstra; Huilin Li
Journal:  Proc Natl Acad Sci U S A       Date:  2010-06-01       Impact factor: 11.205

Review 5.  Precise beam-tilt alignment and collimation are required to minimize the phase error associated with coma in high-resolution cryo-EM.

Authors:  Robert M Glaeser; Dieter Typke; Peter C Tiemeijer; James Pulokas; Anchi Cheng
Journal:  J Struct Biol       Date:  2010-12-21       Impact factor: 2.867

6.  Structure of AAV-DJ, a retargeted gene therapy vector: cryo-electron microscopy at 4.5 Å resolution.

Authors:  Thomas F Lerch; Jason K O'Donnell; Nancy L Meyer; Qing Xie; Kenneth A Taylor; Scott M Stagg; Michael S Chapman
Journal:  Structure       Date:  2012-06-21       Impact factor: 5.006

Review 7.  Reaching the information limit in cryo-EM of biological macromolecules: experimental aspects.

Authors:  Robert M Glaeser; Richard J Hall
Journal:  Biophys J       Date:  2011-05-18       Impact factor: 4.033

8.  High-gradient nanomagnets on cantilevers for sensitive detection of nuclear magnetic resonance.

Authors:  Jonilyn G Longenecker; H J Mamin; Alexander W Senko; Lei Chen; Charles T Rettner; Daniel Rugar; John A Marohn
Journal:  ACS Nano       Date:  2012-10-10       Impact factor: 15.881

9.  Radiation damage effects at four specimen temperatures from 4 to 100 K.

Authors:  Benjamin E Bammes; Joanita Jakana; Michael F Schmid; Wah Chiu
Journal:  J Struct Biol       Date:  2009-11-10       Impact factor: 2.867

10.  EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps.

Authors:  Steffen Lindert; René Staritzbichler; Nils Wötzel; Mert Karakaş; Phoebe L Stewart; Jens Meiler
Journal:  Structure       Date:  2009-07-15       Impact factor: 5.006

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