2jqr

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==Overview==
==Overview==
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The structure of yeast iso-1-cytochrome c has been refined against X-ray diffraction data to a nominal resolution of 1.23 A. The atomic model contains 893 protein atoms, as well as 116 water molecules and one sulfate anion. Also included in the refinement are 886 hydrogen atoms belonging to the protein molecule. The crystallographic R-factor is 0.192 for the 12,513 reflections with F greater than or equal to 3 sigma (F) in the resolution range 6.0 to 1.23 A. Co-ordinate accuracy is estimated to be better than 0.18 A. The iso-1-cytochrome c molecule has the typical cytochrome c fold, with the polypeptide chain organized into a series of alpha-helices and reverse turns that serve to envelop the heme prosthetic group in a hydrophobic pocket. Inspection of the conformations of helices in the molecule shows that the local environments of the helices, in particular the presence of intrahelical threonine residues, cause distortions from ideal alpha-helical geometry. Analysis of the internal mobility of iso-1-cytochrome c, based on refined crystallographic temperature factors, shows that the most rigid parts of the molecule are those that are closely associated with the heme group. The degree of saturation of hydrogen-bonding potential is high, with 90% of all polar atoms found to participate in hydrogen bonding. The geometry of intramolecular hydrogen bonds is typical of that observed in other high-resolution protein structures. The 116 water molecules present in the model represent about 41% of those expected to be present in the asymmetric unit. The majority of the water molecules are organized into a small number of hydrogen-bonding networks that are anchored to the protein surface. Comparison of the structure of yeast iso-1-cytochrome c with those of tuna and rice cytochromes c shows that these three molecules have very high structural similarity, with the atomic packing in the heme crevice region being particularly highly conserved. Large conformational differences that are observed between these cytochromes c can be explained by amino acid substitutions. Additional subtle differences in the positioning of the side-chains of several highly conserved residues are also observed and occur due to unique features in the local environments of each cytochrome c molecule.(ABSTRACT TRUNCATED AT 400 WORDS)
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In the general view of protein-complex formation, a transient and dynamic encounter complex proceeds to form a more stable, well-defined, and active form. In weak protein complexes, however, the encounter state can represent a significant population of the complex. The redox proteins adrenodoxin (Adx) and cytochrome c (C c) associate to form such a weak and short-lived complex, which is nevertheless active in electron transfer. To study the conformational freedom within the protein complex, the native complex has been compared to a cross-linked counterpart by using solution scattering and NMR spectroscopy. Oligomerization behavior of the native complex in solution revealed by small-angle X-ray scattering indicates a stochastic nature of complex formation. For the cross-linked complex, interprotein paramagnetic effects are observed, whereas for the native complex, extensive averaging occurs, consistent with multiple orientations of the proteins within the complex. Simulations show that C c samples about half of the surface area of adrenodoxin. It is concluded that the complex of Adx/C c is entirely dynamic and can be considered as a pure encounter complex.
==About this Structure==
==About this Structure==
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==Reference==
==Reference==
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High-resolution refinement of yeast iso-1-cytochrome c and comparisons with other eukaryotic cytochromes c., Louie GV, Brayer GD, J Mol Biol. 1990 Jul 20;214(2):527-55. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2166169 2166169]
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Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy., Xu X, Reinle W, Hannemann F, Konarev PV, Svergun DI, Bernhardt R, Ubbink M, J Am Chem Soc. 2008 May 21;130(20):6395-403. Epub 2008 Apr 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18439013 18439013]
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Protein complex]]
[[Category: Protein complex]]
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[[Category: Paramagnetic relaxation enhancement]]
[[Category: Paramagnetic relaxation enhancement]]
[[Category: Pseudocontact shift]]
[[Category: Pseudocontact shift]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:37:16 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 11 10:54:17 2008''

Revision as of 07:54, 11 June 2008

Image:2jqr.jpg

Template:STRUCTURE 2jqr

Solution model of crosslinked complex of cytochrome c and adrenodoxin


Overview

In the general view of protein-complex formation, a transient and dynamic encounter complex proceeds to form a more stable, well-defined, and active form. In weak protein complexes, however, the encounter state can represent a significant population of the complex. The redox proteins adrenodoxin (Adx) and cytochrome c (C c) associate to form such a weak and short-lived complex, which is nevertheless active in electron transfer. To study the conformational freedom within the protein complex, the native complex has been compared to a cross-linked counterpart by using solution scattering and NMR spectroscopy. Oligomerization behavior of the native complex in solution revealed by small-angle X-ray scattering indicates a stochastic nature of complex formation. For the cross-linked complex, interprotein paramagnetic effects are observed, whereas for the native complex, extensive averaging occurs, consistent with multiple orientations of the proteins within the complex. Simulations show that C c samples about half of the surface area of adrenodoxin. It is concluded that the complex of Adx/C c is entirely dynamic and can be considered as a pure encounter complex.

About this Structure

2JQR is a Protein complex structure of sequences from Bos taurus and Saccharomyces cerevisiae. Full crystallographic information is available from OCA.

Reference

Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy., Xu X, Reinle W, Hannemann F, Konarev PV, Svergun DI, Bernhardt R, Ubbink M, J Am Chem Soc. 2008 May 21;130(20):6395-403. Epub 2008 Apr 26. PMID:18439013 Page seeded by OCA on Wed Jun 11 10:54:17 2008

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