1kx3: Difference between revisions
No edit summary |
No edit summary |
||
| Line 4: | Line 4: | ||
|PDB= 1kx3 |SIZE=350|CAPTION= <scene name='initialview01'>1kx3</scene>, resolution 2.00Å | |PDB= 1kx3 |SIZE=350|CAPTION= <scene name='initialview01'>1kx3</scene>, resolution 2.00Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=MN:MANGANESE (II) ION'>MN</scene> | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[1aoi|1AOI]], [[1kx4|1KX4]], [[1kx5|1KX5]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kx3 OCA], [http://www.ebi.ac.uk/pdbsum/1kx3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kx3 RCSB]</span> | |||
}} | }} | ||
| Line 28: | Line 31: | ||
[[Category: Richmond, T J.]] | [[Category: Richmond, T J.]] | ||
[[Category: Sargent, D F.]] | [[Category: Sargent, D F.]] | ||
[[Category: chromatin]] | [[Category: chromatin]] | ||
[[Category: histone]] | [[Category: histone]] | ||
| Line 38: | Line 40: | ||
[[Category: supercoiled dna]] | [[Category: supercoiled dna]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:54:50 2008'' | ||
Revision as of 21:54, 30 March 2008
| |||||||
| , resolution 2.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Related: | 1AOI, 1KX4, 1KX5
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
OverviewOverview
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 StructureAbout this Structure
1KX3 is a Protein complex structure of sequences from Homo sapiens and Xenopus laevis. Full crystallographic information is available from OCA.
ReferenceReference
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 Mar 30 21:54:50 2008