7YRD

histone methyltransferase

Summary for 7YRD

• Entry DOI: 10.2210/pdb7yrd/pdb
• EMDB information: 34053
• Descriptor: Histone H3.2, Histone H4, DNA (146-MER), ... (8 entities in total)
• Functional Keywords: histone methyltransferase, gene regulation
• Biological source: Xenopus laevis (African clawed frog); More
• Total number of polymer chains: 11
• Total formula weight: 214807.61

Authors

Li, H.,Wang, W.Y. (deposition date: 2022-08-09, release date: 2023-08-16, Last modification date: 2023-12-13)

Primary citation

Huang, L.,Wang, Y.,Long, H.,Zhu, H.,Wen, Z.,Zhang, L.,Zhang, W.,Guo, Z.,Wang, L.,Tang, F.,Hu, J.,Bao, K.,Zhu, P.,Li, G.,Zhou, Z.
Structural insight into H4K20 methylation on H2A.Z-nucleosome by SUV420H1.
Mol.Cell, 83:2884-2895.e7, 2023

PubMed Abstract: DNA replication ensures the accurate transmission of genetic information during the cell cycle. Histone variant H2A.Z is crucial for early replication origins licensing and activation in which SUV420H1 preferentially recognizes H2A.Z-nucleosome and deposits H4 lysine 20 dimethylation (H4K20me2) on replication origins. Here, we report the cryo-EM structures of SUV420H1 bound to H2A.Z-nucleosome or H2A-nucleosome and demonstrate that SUV420H1 directly interacts with H4 N-terminal tail, the DNA, and the acidic patch in the nucleosome. The H4 (1-24) forms a lasso-shaped structure that stabilizes the SUV420H1-nucleosome complex and precisely projects the H4K20 residue into the SUV420H1 catalytic center. In vitro and in vivo analyses reveal a crucial role of the SUV420H1 KR loop (residues 214-223), which lies close to the H2A.Z-specific residues D97/S98, in H2A.Z-nucleosome preferential recognition. Together, our findings elucidate how SUV420H1 recognizes nucleosomes to ensure site-specific H4K20me2 modification and provide insights into how SUV420H1 preferentially recognizes H2A.Z nucleosome.

PubMed: 37536340
DOI: 10.1016/j.molcel.2023.07.001

Experimental method

ELECTRON MICROSCOPY (3.2 Å)