Three-dimensional architecture of outer- and inner-dynein arms in flagella revealed by cryo-electron tomography and single particle analysis

2008 ◽  
pp. 25-26
Author(s):  
T. Ishikawa ◽  
K. H. Bui ◽  
T. Movassagh ◽  
H. Sakakibara ◽  
K. Oiwa
Keyword(s):  
Single Particle ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Particle Analysis ◽  
Single Particle Analysis ◽  
Cryo Electron Tomography ◽  
Dynein Arms

scholarly journals Phase Contrast Cryo-Electron Tomography and Single Particle Analysis with a New Phase Plate

2014 ◽  
Vol 20 (S3) ◽  
pp. 232-233
Author(s):  
Maryam Khoshouei ◽  
Radostin Danev ◽  
Günther Gerisch ◽  
Maria Ecke ◽  
Juergen Plitzko ◽  
...  
Keyword(s):  
Single Particle ◽  
Phase Contrast ◽  
Electron Tomography ◽  
Particle Analysis ◽  
Phase Plate ◽  
Single Particle Analysis ◽  
Cryo Electron Tomography ◽  
New Phase

scholarly journals Three Dimensional Reconstruction of CFTR Chloride Channel Using Single Particle Analysis

2009 ◽  
Vol 96 (3) ◽  
pp. 468a
Author(s):  
Kazuhiro Mio ◽  
Toshihiko Ogura ◽  
Muneyo Mio ◽  
Hiroyasu Shimizu ◽  
Tzyh-Chang Hwang ◽  
...  
Keyword(s):  
Single Particle ◽  
Chloride Channel ◽  
Three Dimensional ◽  
Particle Analysis ◽  
Single Particle Analysis ◽  
Three Dimensional Reconstruction ◽  
Dimensional Reconstruction

scholarly journals The Resolution in X-ray Crystallography and Single-Particle Cryogenic Electron Microscopy

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 580
Author(s):  
Victor R.A. Dubach ◽  
Albert Guskov
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Single Particle Analysis ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Fourier Transform

X-ray crystallography and single-particle analysis cryogenic electron microscopy are essential techniques for uncovering the three-dimensional structures of biological macromolecules. Both techniques rely on the Fourier transform to calculate experimental maps. However, one of the crucial parameters, resolution, is rather broadly defined. Here, the methods to determine the resolution in X-ray crystallography and single-particle analysis are summarized. In X-ray crystallography, it is becoming increasingly more common to include reflections discarded previously by traditionally used standards, allowing for the inclusion of incomplete and anisotropic reflections into the refinement process. In general, the resolution is the smallest lattice spacing given by Bragg’s law for a particular set of X-ray diffraction intensities; however, typically the resolution is truncated by the user during the data processing based on certain parameters and later it is used during refinement. However, at which resolution to perform such a truncation is not always clear and this makes it very confusing for the novices entering the structural biology field. Furthermore, it is argued that the effective resolution should be also reported as it is a more descriptive measure accounting for anisotropy and incompleteness of the data. In single particle cryo-EM, the situation is not much better, as multiple ways exist to determine the resolution, such as Fourier shell correlation, spectral signal-to-noise ratio and the Fourier neighbor correlation. The most widely accepted is the Fourier shell correlation using a threshold of 0.143 to define the resolution (so-called “gold-standard”), although it is still debated whether this is the correct threshold. Besides, the resolution obtained from the Fourier shell correlation is an estimate of varying resolution across the density map. In reality, the interpretability of the map is more important than the numerical value of the resolution.

scholarly journals Molecular architecture of inner dynein arms in situ in Chlamydomonas reinhardtii flagella

2008 ◽  
Vol 183 (5) ◽  
pp. 923-932 ◽  
Author(s):  
Khanh Huy Bui ◽  
Hitoshi Sakakibara ◽  
Tandis Movassagh ◽  
Kazuhiro Oiwa ◽  
Takashi Ishikawa
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Molecular Architecture ◽  
Heavy Chains ◽  
Distal Side ◽  
Cryo Electron Tomography ◽  
Dynein Arms

The inner dynein arm regulates axonemal bending motion in eukaryotes. We used cryo-electron tomography to reconstruct the three-dimensional structure of inner dynein arms from Chlamydomonas reinhardtii. All the eight different heavy chains were identified in one 96-nm periodic repeat, as expected from previous biochemical studies. Based on mutants, we identified the positions of the AAA rings and the N-terminal tails of all the eight heavy chains. The dynein f dimer is located close to the surface of the A-microtubule, whereas the other six heavy chain rings are roughly colinear at a larger distance to form three dyads. Each dyad consists of two heavy chains and has a corresponding radial spoke or a similar feature. In each of the six heavy chains (dynein a, b, c, d, e, and g), the N-terminal tail extends from the distal side of the ring. To interact with the B-microtubule through stalks, the inner-arm dyneins must have either different handedness or, more probably, the opposite orientation of the AAA rings compared with the outer-arm dyneins.

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