9D3P
167-bp 5S rDNA nucleosome - open I (open only on the downstream side)
Summary for 9D3P
| Entry DOI | 10.2210/pdb9d3p/pdb |
| Related | 9D3K 9D3L 9D3M 9D3N 9D3O 9D3Q 9D3R 9D3S 9D3T |
| EMDB information | 46539 46541 46543 |
| Descriptor | Histone H3.2, Histone H4, Histone H2A type 2-A, ... (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 | 162302.95 |
| Authors | Alegrio Louro, J.,Cruz-Becerra, G.,Kadonaga, J.T.,Leschziner, A.E. (deposition date: 2024-08-11, release date: 2025-08-13, Last modification date: 2025-10-15) |
| 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., 39:1155-1161, 2025 Cited by 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: 40721296DOI: 10.1101/gad.352720.125 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.5 Å) |
Structure validation
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