The three-dimensional structure of a human IgGl immunoglobulin at 4 Å resolution: a computer fit of various structural domains on the electron density map

1982 ◽  
Vol 15 (5) ◽  
pp. 476-481 ◽  
Author(s):  
R. Sarma ◽  
A. G. Laudin
Keyword(s):  
Electron Density ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structural Domains ◽  
Three Dimensional Structure ◽  
Density Map ◽  
Electron Density Map

The low-resolution structure of human muscle aldolase

1981 ◽  
Vol 293 (1063) ◽  
pp. 209-214 ◽  
Keyword(s):  
Domain Structure ◽  
Electron Density ◽  
Heavy Atom ◽  
Three Dimensional ◽  
Human Muscle ◽  
Dimensional Structure ◽  
Density Map ◽  
Electron Density Map ◽  
Spherical Molecule ◽  
Resolution Structure

The three-dimensional structure of human muscle aldolase has been solved at 5 A resolution with the use of two isomorphous heavy atom derivatives. The enzyme’s four subunits are arranged about three mutually perpendicular intersecting twofold axes to form a compact spherical molecule. The subunit boundaries are clearly defined but a possible domain structure is not apparent in this preliminary electron density map.

scholarly journals Bis(μ2-4-nitrophenolato)bis(4-nitrophenolato)di-μ3-oxido-octaphenyltetratin chloroform sesquisolvate [+ solvate]: a tetranuclear stannoxane

IUCrData ◽  
2019 ◽  
Vol 4 (8) ◽  
Author(s):  
Patrick Butler
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Coordination Geometry ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Complex Molecules ◽  
Three Dimensional Structure

The title tetranuclear stannoxane, [Sn4(C6H5)8(C6H4NO3)4O2]·1.5CHCl3·solvent, crystallized with two independent complex molecules, A and B, in the asymmetric unit together with 1.5 molecules of chloroform. There is also a region of disordered electron density, which was corrected for using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18]. The oxo-tin core of each complex is in a planar `ladder' arrangement and each Sn atom is fivefold SnO3C2 coordinated, with one tin centre having an almost perfect square-pyramidal coordination geometry, while the other three Sn centres have distorted shapes. In the crystal, the complex molecules are arranged in layers, composed of A or B complexes, lying parallel to the bc plane. The complex molecules are linked by a number of C—H...O hydrogen bonds within the layers and between the layers, forming a supramolecular three-dimensional structure.

Electron-density maps

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Fourier Transform ◽  
Electron Density ◽  
Three Dimensional ◽  
Two Dimensions ◽  
Unit Cell ◽  
Density Maps ◽  
Wave Cycle ◽  
Density Map ◽  
The Fourier Transform ◽  
Electron Density Map

When everything has been done to make the phases as good as possible, the time has come to examine the image of the structure in the form of an electron-density map. The electron-density map is the Fourier transform of the structure factors (with their phases). If the resolution and phases are good enough, the electron-density map may be interpreted in terms of atomic positions. In practice, it may be necessary to alternate between study of the electron-density map and the procedures mentioned in Chapter 10, which may allow improvements to be made to it. Electron-density maps contain a great deal of information, which is not easy to grasp. Considerable technical effort has gone into methods of presenting the electron density to the observer in the clearest possible way. The Fourier transform is calculated as a set of electron-density values at every point of a three-dimensional grid labelled with fractional coordinates x, y, z. These coordinates each go from 0 to 1 in order to cover the whole unit cell. To present the electron density as a smoothly varying function, values have to be calculated at intervals that are much smaller than the nominal resolution of the map. Say, for example, there is a protein unit cell 50 Å on a side, at a routine resolution of 2Å. This means that some of the waves included in the calculation of the electron density go through a complete wave cycle in 2 Å. As a rule of thumb, to represent this properly, the spacing of the points on the grid for calculation must be less than one-third of the resolution. In our example, this spacing might be 0.6 Å. To cover the whole of the 50 Å unit cell, about 80 values of x are needed; and the same number of values of y and z. The electron density therefore needs to be calculated on an array of 80×80×80 points, which is over half a million values. Although our world is three-dimensional, our retinas are two-dimensional, and we are good at looking at pictures and diagrams in two dimensions.

scholarly journals On the time variability of the HH jet ejection process

2010 ◽  
Vol 6 (S275) ◽  
pp. 392-395
Author(s):  
Fabio De Colle
Keyword(s):  
Large Scale ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Velocity Variation ◽  
Time Variability ◽  
Ejection Process ◽  
Regularization Techniques ◽  
History Of ◽  
Density Map ◽  
Electron Density Map

AbstractTwo-dimensional emission line images of the HH30 jet were recently used (De Colle et al. 2010) to recover the three-dimensional structure of the jet by applying standard tomographic technique (“Tikhonov regularization techniques”). In this paper I show that it is possible to determine the ejection history of the HH30 jet by directly comparing the outcome of numerical simulations with the results of the tomographic inversion. In particular, it is shown that the HH30 jet electron density map is best reproduced by assuming a velocity variation at the base of the jet with a large scale periodicity (with a period of ~3 yrs) added to small scales velocity variation (with periods ≲months).

scholarly journals Building brain network in electron density map determined by micro-CT

2014 ◽  
Vol 70 (a1) ◽  
pp. C1752-C1752
Author(s):  
Rino Saiga ◽  
Susumu Takekoshi ◽  
Naoya Nakamura ◽  
Akihisa Takeuchi ◽  
Kentaro Uesugi ◽  
...  
Keyword(s):  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
Model Building ◽  
Three Dimensional ◽  
Brain Network ◽  
X Ray ◽  
Density Maps ◽  
Density Map ◽  
Electron Density Map

In macromolecular crystallography, an electron density distribution is traced to build a model of the target molecule. We applied this method to model building for electron density maps of a brain network. Human cerebral tissue was stained with heavy atoms [1]. The sample was then analyzed at the BL20XU beamline of SPring-8 to obtain a three-dimensional map of X-ray attenuation coefficients representing the electron density distribution. Skeletonized wire models were built by placing and connecting nodes in the map [2], as shown in the figure below. The model-building procedures were similar to those reported for crystallographic analyses of macromolecular structures, while the neuronal network was automatically traced by using a Sobel filter. Neuronal circuits were then analytically resolved from the skeletonized models. We suggest that X-ray microtomography along with model building in the electron density map has potential as a method for understanding three-dimensional microstructures relevant to biological functions.

scholarly journals HermiteFit: fast-fitting atomic structures into a low-resolution density map using three-dimensional orthogonal Hermite functions

2014 ◽  
Vol 70 (8) ◽  
pp. 2069-2084 ◽  
Author(s):  
Georgy Derevyanko ◽  
Sergei Grudinin
Keyword(s):  
Electron Density ◽  
Cross Correlation ◽  
Three Dimensional ◽  
Hermite Functions ◽  
Low Resolution ◽  
Atomic Structures ◽  
Resolution Electron ◽  
Laplacian Filter ◽  
Density Map ◽  
Electron Density Map

HermiteFit, a novel algorithm for fitting a protein structure into a low-resolution electron-density map, is presented. The algorithm accelerates the rotation of the Fourier image of the electron density by using three-dimensional orthogonal Hermite functions. As part of the new method, an algorithm for the rotation of the density in the Hermite basis and an algorithm for the conversion of the expansion coefficients into the Fourier basis are presented.HermiteFitwas implemented using the cross-correlation or the Laplacian-filtered cross-correlation as the fitting criterion. It is demonstrated that in the Hermite basis the Laplacian filter has a particularly simple form. To assess the quality of density encoding in the Hermite basis, an analytical way of computing the crystallographicRfactor is presented. Finally, the algorithm is validated using two examples and its efficiency is compared with two widely used fitting methods,ADP_EMandcoloresfrom theSituspackage.HermiteFitwill be made available at http://nano-d.inrialpes.fr/software/HermiteFit or upon request from the authors.

scholarly journals Efficient targeting to storage granules of human proinsulins with altered propeptide domain.

1988 ◽  
Vol 106 (6) ◽  
pp. 1843-1851 ◽  
Author(s):  
S K Powell ◽  
L Orci ◽  
C S Craik ◽  
H P Moore
Keyword(s):  
High Efficiency ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structural Domains ◽  
C Peptide ◽  
Three Dimensional Structure ◽  
Morphological Criteria ◽  
Cellular Machinery ◽  
Storage Granules

In neuronal and endocrine cells, peptide hormones are selectively segregated into storage granules, while other proteins are exported continuously without storage. Sorting of hormones by cellular machinery involves the recognition of specific structural domains on prohormone molecules. Since the propeptide of insulin is known to play an important role in its three-dimensional structure, it is reasonable to speculate that targeting of proinsulin to storage granules would require a functional connecting peptide. To test this hypothesis, we constructed two mutations in human proinsulin with different predicted structures. In one mutation, Ins delta C, the entire C peptide was deleted, resulting in an altered insulin in which the B and the A chains are joined contiguously. In the other mutation, Ins/IGF, the C peptide of proinsulin was replaced with the unrelated 12-amino acid connecting peptide of human insulin-like growth factor-I; this substitution should permit correct folding of the B and A chains to form a tertiary structure similar to that of proinsulin. By several biochemical and morphological criteria, we found that Ins/IGF is efficiently targeted to storage granules, suggesting that the C peptide of proinsulin does not contain necessary sorting information. Unexpectedly, Ins delta C, which presumably cannot fold properly, is also targeted to granules at a high efficiency. These results imply that either the targeting machinery can tolerate changes in the tertiary structure of transported proteins, or that the B and A chains of insulin can form a relatively intact three-dimensional structure even in the absence of C peptide.

Effect of Fibrinolytic Compound GDG on Crystal Structure of Lysozyme

2012 ◽  
Vol 554-556 ◽  
pp. 1768-1775
Author(s):  
Yong Xian Wang ◽  
Wen Hui Wu ◽  
Bin Bao ◽  
Rui Rui Song ◽  
Li Chun Sun
Keyword(s):  
Crystal Size ◽  
Main Chain ◽  
Protein Crystallization ◽  
Three Dimensional ◽  
Intrinsic Activity ◽  
Dimensional Structure ◽  
Sodium Acetate Buffer ◽  
Synchrotron Radiation Diffraction ◽  
Density Map ◽  
Electron Density Map

Lysozyme was extensively studied as a model of protein crystallization, we identified that 15 mg/ml lysozyme, 0.1 M sodium acetate buffer containing 5% (w/v) sodium chloride and 0.02% (w/v) sodium azide, pH 5.2, crystal nucleus were less and crystals could reach a certain size. Basic on GDG effected conformation of enzyme which enhancing the reciprocal activation of plasminogen and prourokinase via the elevation of intrinsic activity of prourokinase, we obtained the crystal of lysozyme added α-D-glucopyranoslydiacylglycerol (GDG), GDG: HEWL (c/c) = 2:1, 1:1, 1:2, performed the synchrotron radiation diffraction and collected the three dimensional structure data. It is showing that increased in number of crystal amount and decreased in volume of crystal size in crystallization of lysozyme accompanied by the concentration of GDG. It is not displayed effect on the main chain and most side chains of lysozyme in the presence of GDG in the electron density map.

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