Nucleosome core particle

Reference: Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997). Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 389, 251-60. [Medline abstract]. [Nature website].


The histone core octamer is composed of 4 sets of dimers which interact with each other through the "histone fold". Histone H3 (blue) and Histone H4 (green) interact through one fold to form a heterodimer, Histones H2A (orange) and H2B (red) interact through another histone fold to dimerize. Additional interactions, via 4-helix bundle interactions of histone H3 and H3', form the core H3-H4 tetramer. A pair of homologous interactions of H2B and H4 form the octamer. Fig. 1d) shows one half of the nucleosome.

Histone fold

Each histone monomer has three alpha helices in the shape of a shallow "U". The "histone fold" is an interdigtation of these U's, with the long alpha2 helix of one monomer laying across that of its partner. Fig2a ( ) shows the histone fold of H3 and H4. Additional interactions of the loop regions between helices L1 and L2 help to hold the fold together and are sites for interaction with the DNA backbone. The rest of the DNA binding site comes from the end of helix 1. You can zoom into this region to see Fig2c ( )Hydrogen bonds are indicated by dotted lines. Arg116 of H3 forms 2 H-bonds with asp123. Similarly, arg78 of H4 H-bonds with asp 85.
Fig2b ( ) show the histone fold of H2A and H2B. Most of the interactions are similar to H3-H4, but as seen when you zoom in in Fig2d ( ) arg83 of H2B interacts with DNA rather than with glu90. H2A lacks charged residues at these sites.

The four-helix bundles.

The L2 regions of H3 and H3' interact to form 4 helix bundles (Fig2e) . Both hydrophobic and H-bond interactions are used. His113 of H3' H-bonds with Asp123. Similar interactions between H2B and H4 form another 4 helix bundle (Fig2f) . His75 of H4 H-bonds to Asp90 of H2B.

The Histone tails.

The tail regions of the histones (sites of acetylation and other modifications) protrude between the DNA gyres, as seen in the spacefilling view  .

Back to intro to DNA and RNA structure.

Comments or Suggestions to:Jim Nolan