scholarly journals Sir Aaron Klug OM. 11 August 1926—20 November 2018

2020 ◽  
Vol 68 ◽  
pp. 273-296
Author(s):  
R. A. Crowther
Keyword(s):  
Electron Microscopy ◽  
Molecular Biology ◽  
Royal Society ◽  
Zinc Fingers ◽  
Three Dimensional ◽  
Transfer Rna ◽  
Biological Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atomic Structures

Aaron Klug made outstanding contributions to the development of structural molecular biology. An early interest in viruses, stemming from work with Rosalind Franklin, prompted him to think deeply about extracting the information contained in electron micrographs. As a result, he proposed a method for making three-dimensional maps of biological specimens from the projected images given by micrographs. For this development and its application to complex molecular assemblies, he was awarded the 1982 Nobel Prize in Chemistry. The recent revolution in biological structure determination, whereby atomic structures can now be determined from micrographs of frozen hydrated specimens, derives from this initial breakthrough. With colleagues, Aaron applied X-ray crystallography and electron microscopy to determine the structures and thereby understand the functions of many biological assemblies, including viruses, transfer RNA, chromatin and zinc fingers. He also made important forays into the pathogenesis of Alzheimer's disease and related dementias. Aaron was director of the MRC Laboratory of Molecular Biology in Cambridge from 1986 to 1996 and President of the Royal Society from 1995 to 2000.

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.

Bacteriophage PRD1 Capsid Structure: Iterative Combination of Threedimensional Electron Microscopy and X-Ray Crystallography

2000 ◽  
Vol 6 (S2) ◽  
pp. 284-285
Author(s):  
Carmen San Martin ◽  
Roger M. Burnett ◽  
Felix de Haas ◽  
Ralph Heinkel ◽  
Twan Rutten ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Three Dimensional ◽  
Cyclic Process ◽  
Particle Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Bacteriophage Prd1 ◽  
Cryo Electron Microscopy ◽  
Moderate Resolution ◽  
Protein Rich

PRD1 is a ds-DNA bacteriophage from the Tectiviridae family with an unusual structural feature: the viral genome is enclosed by a protein-rich membrane, which is in turn enclosed by an external icosahedral protein shell (capsid). Three-dimensional reconstructions from cryo-electron microscopy (cryo-EM) images have revealed the structure of the PRD1 capsid at moderate resolution (28 Å), while X-ray crystallographic studies have recently provided a high resolution (1.85 Å) picture of the major coat protein, P3. We have now combined these results from different imaging methods to obtain a more detailed understanding of the virion organization. The combination has been made in a cyclic process: a preliminary fitting of the atomic structure of P3 to each one of its independent positions in the cryo-EM maps of the capsids provided initial models that could be used to improve the reconstructions; the refined maps then served as a base frame for an optimized fit. This process allows us to study the viral particle structure at “quasi-atomic” resolution.

Three-Dimensional Structure Of C3D From Low Temperature Scanning Transmission Electron Microscopy and X-Ray Crystallography

2000 ◽  
Vol 6 (S2) ◽  
pp. 294-295
Author(s):  
D.J. Martin ◽  
F.P. Ottensmeyer
Keyword(s):  
Electron Microscopy ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Rays ◽  
Complement Protein ◽  
X Ray ◽  
X Ray Crystallography ◽  
Scanning Transmission Electron ◽  
Transmission Electron ◽  
Scanning Transmission

Macromolecular structure can be solved by x-ray crystallography to atomic resolution provided that the molecule can be crystallized, that the crystals diffract x-rays to high resolution, and that the phases of the diffracted x-rays can be determined. Though the resolution of single particle imaging by electron microscopy is lower than that of x-ray diffraction by crystals, electron microscopy can directly image a large molecular weight range of macromolecules in a non-crystalline environment, and provide the basis for the three-dimensional reconstruction of these structures. To investigate combining structural information from x-ray crystallography and electron microscopy for unknown structures, we have imaged a small protein of known structure (1), the 35 kDa human complement protein fragment C3d, in a scanning transmission electron microscope (STEM). The intention is to eventually combine the knowledge of electron densities and molecular boundaries from electron microscopy to assist in phase determination in x-ray crystallography.

Preliminary Three-Dimensional Model of Insect Lipoprotein HDLp by Using Electron Microscopy and X-ray Crystallography

2004 ◽  
Vol 10 (S02) ◽  
pp. 1514-1515 ◽  
Author(s):  
Karine M Valentijn ◽  
Roman Koning ◽  
Yvonne Derks ◽  
Jan M Van Doorn ◽  
Theo P Van der Krift ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Three Dimensional ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
X Ray ◽  
X Ray Crystallography

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.

Microtubules, sickle cell hemoglobin fibers, and various crystal structures

1983 ◽  
Vol 41 ◽  
pp. 422-425
Author(s):  
Stuart J. Edelstein ◽  
Richard H. Crepeau ◽  
Christopher W. Akey ◽  
Thomas A. Ceska
Keyword(s):  
Molecular Structure ◽  
Electron Microscopy ◽  
Cytochrome Oxidase ◽  
Sickle Cell ◽  
Three Dimensional ◽  
Beef Heart ◽  
Structural Studies ◽  
Image Reconstruction Techniques ◽  
X Ray ◽  
X Ray Crystallography

Structural studies involving electron microscopy and image reconstruction techniques are now approaching levels of resolution that had previously been the domain of x-ray crystallography. Studies on purple membrane are a prime example. Although few other systems have reached comparable levels of resolution, progress is being made on several fronts. Citing work from this laboratory, I will illustrate three ways we are using electron microscopy to approach the border with x-ray crystallography, in studies on: three-dimensional crystals (cytochrome oxidase from P. aeruginosa, catalase, and beef heart F1-ATPase); arrays of proteins which do not form three-dimensional crystals (tubulin sheets and microtubules); and the supra-molecular structure of a protein of known atomic structure (sickle cell hemoglobin).A. Electron microscopy as an adjunct to X-ray crystallography for threedimensional crystalsOur applications in this area have primarily consisted of embedding and sectioning techniques with crystals that are too small or otherwise unsuitable for x-ray crystallography, such as occur for cytochrome oxidase from P. aeruginosa or beef heart F1-ATPase.

Methodology for determining the three-dimensional crystal structure of myosin Sl from electron microscopy of orthogonal thin sections

1986 ◽  
Vol 44 ◽  
pp. 26-29
Author(s):  
T. S. Baker ◽  
D. A. Winkelmann
Keyword(s):  
Crystal Structure ◽  
Electron Microscopy ◽  
Single Unit ◽  
Three Dimensional ◽  
Detailed Knowledge ◽  
Thin Sections ◽  
X Ray ◽  
X Ray Crystallography ◽  
Density Map ◽  
Dimensional Crystal

Detailed knowledge of the structure of myosin is essential for understanding the mechanism of muscle contraction. The discovery of conditions for crystallizing the head of myosin (Sl = subfragment 1) has led to systematic studies of the SI structure by x-ray crystallography and electron microscopy. We describe the method used to determine the structure of the myosin Sl molecule by electron microscopy (Fig. 3). This method involved independently reconstructing the three-dimensional density of several thin sections obtained from oriented crystals and then combining these reconstructions to produce a final, averaged density map of a single unit cell.

scholarly journals John Thomas Finch. 28 February 1930—5 December 2017

2018 ◽  
Vol 66 ◽  
pp. 183-199
Author(s):  
R. A. Crowther ◽  
K. C. Holmes
Keyword(s):  
Molecular Structure ◽  
Electron Microscopy ◽  
Electron Microscope ◽  
Three Dimensional ◽  
Important Place ◽  
Diverse Range ◽  
X Ray ◽  
X Ray Crystallography ◽  
Embedded Particles ◽  
Team Player

John Finch was a gifted experimentalist who used X-ray crystallography and electron microscopy to elucidate the structures of important biological assemblies, particularly viruses and chromatin. When he started research in the 1950s, little was known about the structure of viruses, and the methods for investigating them were fairly limited. His early work on crystals of viruses was important in establishing their symmetry, and later with the electron microscope he mapped out the molecular structure of many virus coats. His observations on negatively stained preparations demonstrated that images of particles prepared in this way represented projections of fully stained embedded particles, not merely one-sided footprints. This was very relevant to the development of methods for making three-dimensional maps of specimens from electron micrographs. Later, besides further studies of viruses, he worked on many other systems, including chromatin, nucleosomes and tRNA. John was very much a team player and held an important place as the key experimentalist in many influential collaborations, investigating a diverse range of biological specimens.

Max Perutz and the SPSL

2011 ◽  
Author(s):  
Georgina Ferry
Keyword(s):  
Molecular Biology ◽  
Nobel Prize ◽  
Three Dimensional ◽  
Molecular Biologist ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Successful Attempt ◽  
Practical Support ◽  
Protein Molecules

This chapter focuses on Austrian-born molecular biologist Max Perutz (1914–2002). Perutz was one of twenty scientific refugees from continental Europe who went on to win Nobel Prizes. A chemist and molecular biologist, he led the first successful attempt to discover the three-dimensional structure of protein molecules using X-ray crystallography, for which he shared the 1962 Nobel Prize. He was the founding chairman of the Laboratory of Molecular Biology in Cambridge, an institution that continues to thrive and counts thirteen Nobel Prize-winners among those who have spent time in its laboratories. Although Perutz applied to the Society for the Protection of Science and Learning (SPSL) for funding, in the event he did not need their money. His case, however, offers an excellent example of the emotional and practical support SPSL's officers extended to all academics who found themselves in precarious situations in the years following the rise to power of the Nazis in Germany and their subsequent conquest or annexation of neighbouring countries.

scholarly journals MicroED data collection and processing

2015 ◽  
Vol 71 (4) ◽  
pp. 353-360 ◽  
Author(s):  
Johan Hattne ◽  
Francis E. Reyes ◽  
Brent L. Nannenga ◽  
Dan Shi ◽  
M. Jason de la Cruz ◽  
...  
Keyword(s):  
Data Collection ◽  
Three Dimensional ◽  
Limiting Factor ◽  
Structural Studies ◽  
X Ray ◽  
X Ray Crystallography ◽  
Atomic Structures ◽  
Single Well ◽  
Diffraction Patterns ◽  
Three Dimensional Models

MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.

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