5NL0

Crystal structure of a 197-bp palindromic 601L nucleosome in complex with linker histone H1

Summary for 5NL0

• Entry DOI: 10.2210/pdb5nl0/pdb
• Descriptor: Histone H3.2, Histone H4, Histone H2A type 1, ... (7 entities in total)
• Functional Keywords: nucleosome, chromatin, linker histones, histone h1, chromatin binding protein / dna, chromatin binding protein - dna complex
• Biological source: Xenopus laevis (African clawed frog); More
• Cellular location: Nucleus: P84233 P62799 P06897 P02281 P22844
• Total number of polymer chains: 17
• Total formula weight: 426621.04

Authors

Garcia-Saez, I.,Petosa, C.,Dimitrov, S. (deposition date: 2017-04-03, release date: 2017-05-17, Last modification date: 2024-01-17)

Primary citation

Bednar, J.,Garcia-Saez, I.,Boopathi, R.,Cutter, A.R.,Papai, G.,Reymer, A.,Syed, S.H.,Lone, I.N.,Tonchev, O.,Crucifix, C.,Menoni, H.,Papin, C.,Skoufias, D.A.,Kurumizaka, H.,Lavery, R.,Hamiche, A.,Hayes, J.J.,Schultz, P.,Angelov, D.,Petosa, C.,Dimitrov, S.
Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1.
Mol. Cell, 66:384-397.e8, 2017

PubMed Abstract: Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp nucleosome bearing symmetric 25 bp linker DNA arms in complex with vertebrate linker histone H1. We determined electron cryo-microscopy (cryo-EM) and crystal structures of unbound and H1-bound nucleosomes and validated these structures by site-directed protein cross-linking and hydroxyl radical footprinting experiments. Histone H1 shifts the conformational landscape of the nucleosome by drawing the two linkers together and reducing their flexibility. The H1 C-terminal domain (CTD) localizes primarily to a single linker, while the H1 globular domain contacts the nucleosome dyad and both linkers, associating more closely with the CTD-distal linker. These findings reveal that H1 imparts a strong degree of asymmetry to the nucleosome, which is likely to influence the assembly and architecture of higher-order structures.

PubMed: 28475873
DOI: 10.1016/j.molcel.2017.04.012

Experimental method

X-RAY DIFFRACTION (5.4 Å)