7XPX

Cryo-EM structure of the histone methyltransferase SET8 bound to H4K20Ecx-nucleosome

Summary for 7XPX

• Entry DOI: 10.2210/pdb7xpx/pdb
• EMDB information: 33385
• Descriptor: Histone H3, Histone H4, Histone H2A, ... (8 entities in total)
• Functional Keywords: methyltransferase, nucleosome, nuclear protein-dna complex, nuclear protein/dna
• Biological source: Xenopus laevis (African clawed frog); More
• Total number of polymer chains: 11
• Total formula weight: 223406.61

Authors

Shi, L.X.,Zhou, Z. (deposition date: 2022-05-06, release date: 2022-06-01)

Primary citation

Shi, L.,Huang, L.,Long, H.,Song, A.,Zhou, Z.
Structural basis of nucleosomal H4K20 methylation by methyltransferase SET8.
Faseb J., 36:e22338-e22338, 2022

PubMed Abstract: Histone H4 lysine 20 monomethylation (H4K20me1) plays a crucial role in multiple processes including DNA damage repair, DNA replication, and cell cycle control. Histone methyltransferase SET8 (previously named PR-Set7/KMT5A) mediates the chromatin deposition of H4K20me1, but how SET8 recognizes and modifies H4 in the context of the nucleosome is not fully understood. Here, we developed a simple chemical modification approach for H4K20 substitution by using the lysine analog S-ethyl-L-cysteine (Ecx). Substitution of H4K20 with H4Ecx20 improves the stability of the SET8-nucleosome complex, allowing us to determine the cryo-EM structure at 3.2 Å resolution. Structural analyses show that SET8 directly interacts with the H4 tail and the H2A-H2B acidic patch to ensure nucleosome binding. SET8 residues R339, K341, K351 make contact with nucleosomal DNA at the super helical location 2 (SHL2). Substitution of SET8 DNA-binding residues with alanines decreases the SET8-nucleosome interaction and impairs the methyltransferase activity. Disrupting the binding between SET8 R192 and H2A-H2B acidic patch decreases the cellular level of H4K20me1. Together, these results reveal a near-atomic resolution structure of SET8-bound nucleosome and provide insights into the SET8-mediated H4K20 recognition and modification. The lysine-to-Ecx substitution approach can be applied to the study of other methyltransferases.

PubMed: 35532550
DOI: 10.1096/fj.202101821R

Experimental method

ELECTRON MICROSCOPY (3.2 Å)