High-resolution structure of the native histone octamer.

Crystals of native histone octamers (H2A-H2B)-(H4-H3)-(H3'-H4')-(H2B'-H2A') from chick erythrocytes in 2 M KCl, 1.35 M potassium phosphate pH 6.9 diffract X-rays to 1.90 A resolution, yielding a structure with an R(work) value of 18.7% and an Rfree of 22.2%. The crystal space group is P6(5), the asymmetric unit of which contains one complete octamer. This high-resolution model of the histone-core octamer allows further insight into intermolecular interactions, including water molecules, that dock the histone dimers to the tetramer in the nucleosome-core particle and have relevance to nucleosome remodelling. The three key areas analysed are the H2A'-H3-H4 molecular cluster (also H2A-H3'-H4'), the H4-H2B' interaction (also H4'-H2B) and the H2A'-H4 beta-sheet interaction (also H2A-H4'). The latter of these three regions is important to nucleosome remodelling by RNA polymerase II, as it is shown to be a likely core-histone binding site, and its disruption creates an instability in the nucleosome-core particle. A majority of the water molecules in the high-resolution octamer have positions that correlate to similar positions in the high-resolution nucleosome-core particle structure, suggesting that the high-resolution octamer model can be used for comparative studies with the high-resolution nucleosome-core particle.

[1]  Alexey G. Murzin,et al.  Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9 , 2002, Nature.

[2]  M.Mitchell Smith,et al.  Histone octamer function in vivo: mutations in the dimer–tetramer interfaces disrupt both gene activation and repression , 1997, The EMBO journal.

[3]  K. Luger,et al.  Nucleosome Assembly Protein 1 Exchanges Histone H2A-H2B Dimers and Assists Nucleosome Sliding* , 2005, Journal of Biological Chemistry.

[4]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[5]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[6]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.

[7]  J. O. Thomas.  Chromatin structure. , 1977, Biochemical Society symposium.

[8]  D. Rhodes,et al.  Eukaryotic RNA polymerase II binds to nucleosome cores from transcribed genes , 1983, Nature.

[9]  G. Orphanides,et al.  FACT, a Factor that Facilitates Transcript Elongation through Nucleosomes , 1998, Cell.

[10]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[11]  T. Formosa,et al.  Spt16 and Pob3 of Saccharomyces cerevisiae form an essential, abundant heterodimer that is nuclear, chromatin-associated, and copurifies with DNA polymerase alpha. , 1999, Biochemistry.

[12]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[13]  W. Kabsch.  A solution for the best rotation to relate two sets of vectors , 1976 .

[14]  Pieter F. W. Stouten,et al.  Fast prediction and visualization of protein binding pockets with PASS , 2000, J. Comput. Aided Mol. Des..

[15]  T. Richmond,et al.  Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. , 2002, Journal of molecular biology.

[16]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[17]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[18]  E A Merritt,et al.  Raster3D: photorealistic molecular graphics. , 1997, Methods in enzymology.