What we have learned from ribosome structures

2008 ◽  
Vol 36 (4) ◽  
pp. 567-574 ◽  
Author(s):  
V. Ramakrishnan
Keyword(s):  
High Resolution ◽  
Ribosomal Subunit ◽  
Ribosomal Subunits ◽  
30S Subunit ◽  
High Resolution Structure ◽  
70S Ribosome ◽  
Year 2000 ◽  
Resolution Structure

The determination of the high-resolution structures of ribosomal subunits in the year 2000 and of the entire ribosome a few years later are revolutionizing our understanding of the role of the ribosome in translation. In the present article, I summarize the main contributions from our laboratory to this worldwide effort. These include the determination of the structure of the 30S ribosomal subunit and its complexes with antibiotics, the role of the 30S subunit in decoding, and the high-resolution structure of the entire 70S ribosome complexed with mRNA and tRNA.

scholarly journals Tricks of the trade used to accelerate high-resolution structure determination of membrane proteins

FEBS Letters ◽  
2010 ◽  
Vol 584 (12) ◽  
pp. 2539-2547 ◽  
Author(s):  
Yo Sonoda ◽  
Alex Cameron ◽  
Simon Newstead ◽  
Hiroshi Omote ◽  
Yoshinori Moriyama ◽  
...  
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Structure Determination ◽  
High Resolution Structure ◽  
Resolution Structure

scholarly journals High Resolution Structure of the Large Ribosomal Subunit from a Mesophilic Eubacterium

Cell ◽  
2001 ◽  
Vol 107 (5) ◽  
pp. 679-688 ◽  
Author(s):  
Joerg Harms ◽  
Frank Schluenzen ◽  
Raz Zarivach ◽  
Anat Bashan ◽  
Sharon Gat ◽  
...  
Keyword(s):  
High Resolution ◽  
Ribosomal Subunit ◽  
Large Ribosomal Subunit ◽  
High Resolution Structure ◽  
Resolution Structure

High-resolution structure ofBombyx morilipoprotein 7: crystallographic determination of the identity of the protein and its potential role in detoxification

2012 ◽  
Vol 68 (9) ◽  
pp. 1140-1151 ◽  
Author(s):  
Agnieszka J. Pietrzyk ◽  
Santosh Panjikar ◽  
Anna Bujacz ◽  
Jochen Mueller-Dieckmann ◽  
Malgorzata Lochynska ◽  
...  
Keyword(s):  
High Resolution ◽  
Potential Role ◽  
High Resolution Structure ◽  
Resolution Structure

scholarly journals High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Mark A. Herzik ◽  
Mengyu Wu ◽  
Gabriel C. Lander
Keyword(s):  
High Resolution ◽  
Structure Determination ◽  
High Resolution Structure ◽  
Resolution Structure

scholarly journals High Resolution Structure Determination of Amyloid Fibrils

2018 ◽  
Vol 114 (3) ◽  
pp. 185a
Author(s):  
Robert G. Griffin
Keyword(s):  
High Resolution ◽  
Structure Determination ◽  
Amyloid Fibrils ◽  
High Resolution Structure ◽  
Resolution Structure

scholarly journals High-resolution structure determination of sub-100 kilodalton complexes using conventional cryo-EM

2018 ◽  
Author(s):  
Mark A. Herzik ◽  
Mengyu Wu ◽  
Gabriel C. Lander
Keyword(s):  
High Resolution ◽  
Structure Determination ◽  
Drug Target ◽  
Phase Plate ◽  
Biological Macromolecules ◽  
Cryo Electron Microscopy ◽  
Transmission Electron ◽  
High Resolution Structure ◽  
Resolution Structure

Determining high-resolution structures of biological macromolecules with masses of less than 100 kilodaltons (kDa) has long been a goal of the cryo-electron microscopy (cryo-EM) community. While the Volta Phase Plate has enabled cryo-EM structure determination of biological specimens of this size range, use of this instrumentation is not yet fully automated and can present technical challenges. Here, we show that conventional defocus-based cryo-EM methodologies can be used to determine the high-resolution structures of specimens amassing less than 100 kDa using a transmission electron microscope operating at 200 keV coupled with a direct electron detector. Our ~2.9 Å structure of alcohol dehydrogenase (82 kDa) proves that bound ligands can be resolved with high fidelity, indicating that these methodologies can be used to investigate the molecular details of drug-target interactions. Our ~2.8 Å and ~3.2 Å resolution structures of methemoglobin demonstrate that distinct conformational states can be identified within a dataset for proteins as small as 64 kDa. Furthermore, we provide the first sub-nanometer cryo-EM structure of a protein smaller than 50 kDa.

scholarly journals Devitrification reduces beam-induced movement in cryo-EM

IUCrJ ◽  
2021 ◽  
Vol 8 (2) ◽  
pp. 186-194
Author(s):  
Jan-Philip Wieferig ◽  
Deryck J. Mills ◽  
Werner Kühlbrandt
Keyword(s):  
High Resolution ◽  
Structure Determination ◽  
High Energy ◽  
Full Potential ◽  
High Energy Electrons ◽  
High Resolution Structure ◽  
Image Blurring ◽  
Particle Images ◽  
Resolution Structure

As cryo-EM approaches the physical resolution limits imposed by electron optics and radiation damage, it becomes increasingly urgent to address the issues that impede high-resolution structure determination of biological specimens. One of the persistent problems has been beam-induced movement, which occurs when the specimen is irradiated with high-energy electrons. Beam-induced movement results in image blurring and loss of high-resolution information. It is particularly severe for biological samples in unsupported thin films of vitreous water. By controlled devitrification of conventionally plunge-frozen samples, the suspended film of vitrified water was converted into cubic ice, a polycrystalline, mechanically stable solid. It is shown that compared with vitrified samples, devitrification reduces beam-induced movement in the first 5 e Å−2 of an exposure by a factor of ∼4, substantially enhancing the contribution of the initial, minimally damaged frames to a structure. A 3D apoferritin map reconstructed from the first frames of 20 000 particle images of devitrified samples resolved undamaged side chains. Devitrification of frozen-hydrated specimens helps to overcome beam-induced specimen motion in single-particle cryo-EM, as a further step towards realizing the full potential of cryo-EM for high-resolution structure determination.

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