9K43

Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA (C2 symmetry)

Summary for 9K43

• Entry DOI: 10.2210/pdb9k43/pdb
• EMDB information: 62041 62042
• Descriptor: Histone H3.1, Histone H4, Probable histone H2A variant 3, ... (6 entities in total)
• Functional Keywords: nucleosome, histone, h2a.z, arabidopsis, nuclear protein/dna, nuclear protein-dna complex
• Biological source: Arabidopsis thaliana (thale cress); More
• Total number of polymer chains: 10
• Total formula weight: 205706.67

Authors

Wang, Y.,Dong, A. (deposition date: 2024-10-21, release date: 2025-05-14, Last modification date: 2025-05-28)

Primary citation

Wang, Y.,Wu, J.,Yang, S.,Li, X.,Wang, J.,Lv, Q.,Zhu, X.,Lu, G.,Zhang, J.,Shen, W.H.,Liu, B.,Lin, J.,Dong, A.
Structural and functional interrelationships of histone H2A with its variants H2A.Z and H2A.W in Arabidopsis.
Structure, 2025

PubMed Abstract: Multiple histone H2A variants are known in eukaryotes. However, the functional relationship between H2A and its variants in plants remains largely obscure. Using CRISPR-Cas9 editing, we generated a mutant lacking four H2A isoforms in Arabidopsis and analyzed the functional and structural relationships between H2A, H2A.Z, and H2A.W. RNA sequencing and phenotype analyses revealed mild changes in gene transcription and plant development in mutants lacking H2A, H2A.Z, or H2A.W compared with the wild-type plants. Chromatin immunoprecipitation sequencing analysis showed that H2A can substitute for both H2A.Z and H2A.W across the genome, including in euchromatin and heterochromatin regions. However, H2A.Z replaced both H2A and H2A.W primarily within the euchromatin regions. By using DNA and histones from Arabidopsis, we constructed nucleosomes containing H2A, H2A.Z, or H2A.W and resolved their cryogenic electron microscopy (cryo-EM) structures at near-atomic resolution. Collectively, the results reveal the structural similarity and functional redundancy of H2A and its variants in Arabidopsis.

PubMed: 40359943
DOI: 10.1016/j.str.2025.04.015

Experimental method

ELECTRON MICROSCOPY (2.87 Å)