An All-Atom Model of the Chromatin Fiber Containing Linker Histones Reveals a Versatile Structure Tuned by the Nucleosomal Repeat Length
Figure 3
Structures of the chromatin fiber for different NRL.
A) All-atom models of the 7 chromatin fibers obtained by H5-induced folding of a regular chromatin array [7]. For clarity, DNA is shown as a tube. The yellow color corresponds to linkers whereas nucleosomal DNA is presented in pink. Molecular surfaces of H5 globular domains are shown in white. Each structure corresponds to a different NRL. From left to right: 177 bp, 5Rl; 187 bp, 4Rl; 197 bp, 3Rr; 207 bp, 2Rl; 217 bp, 4Rl; 227 bp, 3Ll; 227 bp, 2Lr. For 177 to 207 bp NRL, one DNA repeat length is shown in color (blue, purple, green and orange for 177, 187, 197, and 207 bp NRL respectively). B) Close-up of the four chromatosomes presented in color in A. C- and N-terminal tail extensions are presented in light pink and yellow respectively. The H5 globular domain residues that interact with entry and exit DNA linkers are colored in blue and red. The residues that are interacting with nucleosomal DNA at the dyad axis are colored in green. C) Molecular details of the GH5 positioned on a nucleosome (for 177 and 187 bp NRL). The residues involved in DNA binding [25]–[27] are shown in licorice. In blue: residues interacting with one DNA linker; in red: residues interacting with the other DNA linker; in green: residues inserted into the DNA major groove next to the dyad axis. R47, shown in cyan is never found in contact with DNA.