在高分辨率单颗粒重建中校正埃瓦尔德球。
Correcting for the ewald sphere in high-resolution single-particle reconstructions.
作者信息
Leong Peter A, Yu Xuekui, Zhou Z Hong, Jensen Grant J
机构信息
Department of Applied Physics, California Institute of Technology, Pasadena, California, USA.
出版信息
Methods Enzymol. 2010;482:369-80. doi: 10.1016/S0076-6879(10)82015-4.
Abstract
To avoid the challenges of crystallization and the size limitations of NMR, it has long been hoped that single-particle cryo-electron microscopy (cryo-EM) would eventually yield atomically interpretable reconstructions. For the most favorable class of specimens (large icosahedral viruses), one of the key obstacles is curvature of the Ewald sphere, which leads to a breakdown of the Projection Theorem used by conventional three-dimensional (3D) reconstruction programs. Here, we review the basic problem and our implementation of the "paraboloid" reconstruction method, which overcomes the limitation by averaging information from images recorded from different points of view.
摘要
为避免结晶带来的挑战以及核磁共振（NMR）的尺寸限制，长期以来人们一直希望单颗粒冷冻电子显微镜（cryo-EM）最终能够产生可进行原子水平解释的重构结果。对于最有利的一类标本（大型二十面体病毒），关键障碍之一是埃瓦尔德球的曲率，这会导致传统三维（3D）重构程序所使用的投影定理失效。在此，我们回顾这一基本问题以及我们对“抛物面”重构方法的实现，该方法通过对从不同视角记录的图像信息进行平均来克服这一限制。
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本文引用的文献
1
FREALIGN: high-resolution refinement of single particle structures.
J Struct Biol. 2007 Jan;157(1):117-25. doi: 10.1016/j.jsb.2006.05.004. Epub 2006 Jun 2.
2
Ewald sphere correction for single-particle electron microscopy.
Ultramicroscopy. 2006 Mar;106(4-5):376-82. doi: 10.1016/j.ultramic.2005.11.001. Epub 2005 Dec 9.
3
VIPERdb: a relational database for structural virology.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D386-9. doi: 10.1093/nar/gkj032.
4
Refined structure of the nicotinic acetylcholine receptor at 4A resolution.
J Mol Biol. 2005 Mar 4;346(4):967-89. doi: 10.1016/j.jmb.2004.12.031. Epub 2005 Jan 25.
5
UCSF Chimera--a visualization system for exploratory research and analysis.
J Comput Chem. 2004 Oct;25(13):1605-12. doi: 10.1002/jcc.20084.
6
IMIRS: a high-resolution 3D reconstruction package integrated with a relational image database.
J Struct Biol. 2002 Mar;137(3):292-304. doi: 10.1016/s1047-8477(02)00014-x.
7
Bsoft: image and molecular processing in electron microscopy.
J Struct Biol. 2001 Feb-Mar;133(2-3):156-69. doi: 10.1006/jsbi.2001.4339.
8
Correction of high-resolution data for curvature of the Ewald sphere.
Ultramicroscopy. 2000 Mar;81(2):83-98. doi: 10.1016/s0304-3991(99)00120-5.
9
Defocus-gradient corrected back-projection.
Ultramicroscopy. 2000 Jul;84(1-2):57-64. doi: 10.1016/s0304-3991(00)00005-x.
10
Structure of the reovirus core at 3.6 A resolution.
Nature. 2000 Apr 27;404(6781):960-7. doi: 10.1038/35010041.
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