7VZ4

Cryo-EM structure of human nucleosome core particle composed of the Widom 601L DNA sequence

Summary for 7VZ4

• Entry DOI: 10.2210/pdb7vz4/pdb
• EMDB information: 32220
• Descriptor: Histone H3.1, Histone H4, Histone H2A type 1-B/E, ... (6 entities in total)
• Functional Keywords: nucleosome, chromatin, nuclear protein, nuclear protein-dna complex, nuclear protein/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 10
• Total formula weight: 201637.01

Authors

Takizawa, Y.,Ho, C.-H.,Sato, S.,Danev, R.,Kurumizaka, H. (deposition date: 2021-11-15, release date: 2023-05-17, Last modification date: 2026-09-16)

Primary citation

Takizawa, Y.,Ho, C.H.,Sato, S.,Danev, R.,Kurumizaka, H.
High-Resolution Cryo-EM Analyses of Nucleosomes.
Methods Mol.Biol., 2919:91-107, 2025

PubMed Abstract: The fundamental chromatin unit is the nucleosome, in which approximately 150 base pairs of DNA are bound to the surface of a symmetric histone octamer containing 2 copies each of histones H2A, H2B, H3, and H4. Over the years, numerous structures of nucleosomes have been determined by X-ray crystallography. However, their structural and functional versatility may not have been fully revealed, due to crystal packing effects. Various structures of nucleosomes and their complexes with nucleosome-binding proteins are now being determined by cryo-electron microscopy (cryo-EM) single-particle analysis, allowing the visualization of their structural diversity. In this report, we present a method for high-resolution structural analyses of nucleosomes by cryo-EM and describe the detailed procedures for nucleosome purification, cryo-EM grid preparation, data collection, and data processing. This method can serve as a good starting point for cryo-EM investigations of nucleosomes and their wide range of complexes.

PubMed: 40257559
DOI: 10.1007/978-1-0716-4486-7_6

Experimental method

ELECTRON MICROSCOPY (1.89 Å)