9D3R

147-bp 5S rDNA nucleosome - closed

Summary for 9D3R

• Entry DOI: 10.2210/pdb9d3r/pdb
• Related: 9D3K 9D3L 9D3M 9D3N 9D3O 9D3P 9D3Q 9D3S 9D3T
• EMDB information: 46539 46541 46545
• Descriptor: Histone H3.2, Histone H4, Histone H2B type 1-K, ... (6 entities in total)
• Functional Keywords: 5s rdna nucleosome, natural nucleosome positioning sequence, dna sequence-dependent breathing, gene regulation, gene regulation-dna complex, gene regulation/dna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 10
• Total formula weight: 175185.69

Authors

Alegrio Louro, J.,Cruz-Becerra, G.,Kadonaga, J.T.,Leschziner, A.E. (deposition date: 2024-08-11, release date: 2025-08-13)

Primary citation

Alegrio-Louro, J.,Cruz-Becerra, G.,Kassavetis, G.A.,Kadonaga, J.T.,Leschziner, A.E.
Structural basis of nucleosome recognition by the conserved Dsup and HMGN nucleosome-binding motif.
Genes Dev., 2025

PubMed Abstract: The tardigrade damage suppressor (Dsup) and vertebrate high-mobility group N (HMGN) proteins bind specifically to nucleosomes via a conserved motif whose structure has not been experimentally determined. Here we used cryo-EM to show that both proteins bind to the nucleosome acidic patch via analogous arginine anchors with one molecule bound to each face of the nucleosome. We additionally used the natural promoter-containing 5S rDNA sequence for structural analysis of the nucleosome. These structures of an ancient nucleosome-binding motif suggest that there is an untapped realm of proteins with a related mode of binding to chromatin.

PubMed: 40721296
DOI: 10.1101/gad.352720.125

Experimental method

ELECTRON MICROSCOPY (3.3 Å)