8AAG

H1-bound palindromic nucleosome, state 1

Summary for 8AAG

• Entry DOI: 10.2210/pdb8aag/pdb
• EMDB information: 15143 15144 15146 15147 15156 15168 15169 15170 15171 15172 15173 15232
• Descriptor: DNA/RNA (185-MER), Histone H1.0-B, Histone H3.2, ... (7 entities in total)
• Functional Keywords: linker histone h1, nucleosome, gene regulation
• Biological source: synthetic construct; More
• Total number of polymer chains: 11
• Total formula weight: 252692.33

Authors

Alegrio Louro, J.,Beinsteiner, B.,Cheng, T.C.,Patel, A.K.M.,Boopathi, R.,Angelov, D.,Hamiche, A.,Bednar, J.,Kale, S.,Dimitrov, S.,Klaholz, B. (deposition date: 2022-07-01, release date: 2022-12-14, Last modification date: 2024-07-24)

Primary citation

Louro, J.A.,Boopathi, R.,Beinsteiner, B.,Mohideen Patel, A.K.,Cheng, T.C.,Angelov, D.,Hamiche, A.,Bendar, J.,Kale, S.,Klaholz, B.P.,Dimitrov, S.
Nucleosome dyad determines the H1 C-terminus collapse on distinct DNA arms.
Structure, 31:201-, 2023

PubMed Abstract: Nucleosomes are symmetric structures. However, binding of linker histones generates an inherently asymmetric H1-nucleosome complex, and whether this asymmetry is transmitted to the overall nucleosome structure, and therefore also to chromatin, is unclear. Efforts to investigate potential asymmetry due to H1s have been hampered by the DNA sequence, which naturally differs in each gyre. To overcome this issue, we designed and analyzed by cryo-EM a nucleosome reconstituted with a palindromic (601L) 197-bp DNA. As in the non-palindromic 601 sequence, H1 restricts linker DNA flexibility but reveals partial asymmetrical unwrapping. However, in contrast to the non-palindromic nucleosome, in the palindromic nucleosome H1 CTD collapses to the proximal linker. Molecular dynamics simulations show that this could be dictated by a slightly tilted orientation of the globular domain (GD) of H1, which could be linked to the DNA sequence of the nucleosome dyad.

PubMed: 36610392
DOI: 10.1016/j.str.2022.12.005

Experimental method

ELECTRON MICROSCOPY (10 Å)