3b6f

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[[Image:3b6f.jpg|left|200px]]
[[Image:3b6f.jpg|left|200px]]
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{{Structure
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<!--
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|PDB= 3b6f |SIZE=350|CAPTION= <scene name='initialview01'>3b6f</scene>, resolution 3.450&Aring;
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The line below this paragraph, containing "STRUCTURE_3b6f", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY=
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or leave the SCENE parameter empty for the default display.
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|GENE= LOC494591 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 Xenopus laevis])
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-->
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|DOMAIN=
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{{STRUCTURE_3b6f| PDB=3b6f | SCENE= }}
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|RELATEDENTRY=[[1kx5|1KX5]], [[3b6g|3B6G]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3b6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b6f OCA], [http://www.ebi.ac.uk/pdbsum/3b6f PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3b6f RCSB]</span>
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}}
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'''Nucleosome core particle treated with cisplatin'''
'''Nucleosome core particle treated with cisplatin'''
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[[Category: Davey, C A.]]
[[Category: Davey, C A.]]
[[Category: Wu, B.]]
[[Category: Wu, B.]]
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[[Category: acetylation]]
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[[Category: Acetylation]]
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[[Category: anti-cancer]]
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[[Category: Anti-cancer]]
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[[Category: chromatin]]
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[[Category: Chromatin]]
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[[Category: chromosomal protein]]
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[[Category: Chromosomal protein]]
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[[Category: cisplatin]]
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[[Category: Cisplatin]]
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[[Category: dna-binding]]
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[[Category: Dna-binding]]
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[[Category: drug]]
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[[Category: Drug]]
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[[Category: methylation]]
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[[Category: Methylation]]
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[[Category: nucleosome]]
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[[Category: Nucleosome]]
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[[Category: nucleosome core]]
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[[Category: Nucleosome core]]
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[[Category: nucleus]]
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[[Category: Nucleus]]
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[[Category: phosphorylation]]
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[[Category: Phosphorylation]]
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[[Category: platinum adduct]]
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[[Category: Platinum adduct]]
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[[Category: structural protein/dna complex]]
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[[Category: Structural protein/dna complex]]
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[[Category: ubl conjugation]]
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[[Category: Ubl conjugation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 20:26:11 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:23:29 2008''
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Revision as of 17:26, 4 May 2008

Image:3b6f.jpg

Template:STRUCTURE 3b6f

Nucleosome core particle treated with cisplatin


Overview

Solvent binding in the nucleosome core particle containing a 147 base pair, defined-sequence DNA is characterized from the X-ray crystal structure at 1.9 A resolution. A single-base-pair increase in DNA length over that used previously results in substantially improved clarity of the electron density and accuracy for the histone protein and DNA atomic coordinates. The reduced disorder has allowed for the first time extensive modeling of water molecules and ions. Over 3000 water molecules and 18 ions have been identified. Water molecules acting as hydrogen-bond bridges between protein and DNA are approximately equal in number to the direct hydrogen bonds between these components. Bridging water molecules have a dual role in promoting histone-DNA association not only by providing further stability to direct protein-DNA interactions, but also by enabling formation of many additional interactions between more distantly related elements. Water molecules residing in the minor groove play an important role in facilitating insertion of arginine side-chains. Water structure at the interface of the histones and DNA provides a means of accommodating intrinsic DNA conformational variation, thus limiting the sequence dependency of nucleosome positioning while enhancing mobility. Monovalent anions are bound near the N termini of histone alpha-helices that are not occluded by DNA phosphate groups. Their location in proximity to the DNA phosphodiester backbone suggests that they damp the electrostatic interaction between the histone proteins and the DNA. Divalent cations are bound at specific sites in the nucleosome core particle and contribute to histone-histone and histone-DNA interparticle interactions. These interactions may be relevant to nucleosome association in arrays.

About this Structure

3B6F is a Protein complex structure of sequences from Homo sapiens and Xenopus laevis. Full crystallographic information is available from OCA.

Reference

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution., Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, J Mol Biol. 2002 Jun 21;319(5):1097-113. PMID:12079350 Page seeded by OCA on Sun May 4 20:26:11 2008

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OCA

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