8RGM

Cryo-EM structure of nucleosome containing Widom603 DNA

Summary for 8RGM

• Entry DOI: 10.2210/pdb8rgm/pdb
• EMDB information: 19134
• Descriptor: Histone H3.1, Histone H4, Histone H2A type 1-B/E, ... (6 entities in total)
• Functional Keywords: nucleosome, histone complex, dna binding protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 10
• Total formula weight: 198330.22

Authors

Motorin, N.A.,Afonin, D.,Armeev, G.A.,Moiseenko, A.,Zhao, L.,Vasiliev, V.,Oleinikov, P.,Shaytan, A.,Shi, X.,Studitsky, V.,Sokolova, O. (deposition date: 2023-12-14, release date: 2025-01-01, Last modification date: 2025-05-14)

Primary citation

Armeev, G.A.,Moiseenko, A.V.,Motorin, N.A.,Afonin, D.A.,Zhao, L.,Vasilev, V.A.,Oleinikov, P.D.,Glukhov, G.S.,Peters, G.S.,Studitsky, V.M.,Feofanov, A.V.,Shaytan, A.K.,Shi, X.,Sokolova, O.S.
Structure and dynamics of a nucleosome core particle based on Widom 603 DNA sequence.
Structure, 33:948-, 2025

PubMed Abstract: Nucleosomes are fundamental elements of chromatin organization that participate in compacting genomic DNA and serve as targets for the binding of numerous regulatory proteins. Currently, over 500 different nucleosome structures are known. Despite the large number of nucleosome structures, all of them were formed on only about twenty different DNA sequences. Using cryo-electron microscopy, we determined the structure of the nucleosome formed on a high-affinity Widom 603 DNA sequence at 4 Å resolution; an atomic model was built. We proposed an integrative modeling approach to study the nucleosomal DNA unwrapping based on the cryoelectron microscopy (cryo-EM) data. We also demonstrated the DNA unwrapping of the Widom 603 nucleosome using small angle X-ray scattering and single particle Förster resonance energy transfer measurements. Our results are consistent with the asymmetry of nucleosomal DNA unwrapping. Our data revealed the dependence of nucleosome structure and dynamics on the sequence of nucleosomal DNA.

PubMed: 40101710
DOI: 10.1016/j.str.2025.02.007

Experimental method

ELECTRON MICROSCOPY (4 Å)