9ZEN

Competition for different elements of the nucleosome acidic patch yields distinct functional outcomes. VHH 1B2

Summary for 9ZEN

• Entry DOI: 10.2210/pdb9zen/pdb
• EMDB information: 74113
• Descriptor: Histone H3.2, Histone H4, Histone H2A type 1-B/E, ... (7 entities in total)
• Functional Keywords: chromatin, nucleosome, vhh, antibody, acidic-patch, ap, de novo protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 12
• Total formula weight: 201559.08

Authors

Chakraborty, U.,Saccone, E.C.,Becerra, G.C.,Khan, L.F.,Arslanovic, N.,Aguilar, R.,Gloor, S.L.,Hunt, S.R.,Folkwein, H.J.,Husby, N.L.,Maier, K.E.,Marunde, M.R.,Schomburg, N.K.,Vaidya, A.,Cowles, M.W.,Venters, B.J.,Kassavetis, G.,Sun, Z.-W.,Kadonaga, J.T.,Armache, J.-P.,Keogh, M.-C.,Tyler, J.K. (deposition date: 2025-11-30, release date: 2026-03-04, Last modification date: 2026-07-22)

Primary citation

Chakraborty, U.,Saccone, E.C.,Cruz-Becerra, G.,Khan, L.F.,Arslanovic, N.,Aguilar, R.,Gloor, S.L.,Hunt, S.R.,Folkwein, H.J.,Husby, N.L.,Maier, K.E.,Marunde, M.R.,Schomburg, N.K.,Vaidya, A.,Cowles, M.W.,Venters, B.J.,Kassavetis, G.,Sun, Z.W.,Kadonaga, J.T.,Armache, J.P.,Keogh, M.C.,Tyler, J.K.
Different modes of engagement with the nucleosome acidic patch yield distinct functional outcomes.
Nucleic Acids Res., 54:-, 2026

PubMed Abstract: The nucleosome acidic patch is a hub of coordinated engagement by proteins that regulate genomic function. Here, we report that Saccharomyces cerevisiae Dot5 contains an arginine-rich HMGN-like motif that mediates nucleosome acidic patch binding and is required for the cell growth, DNA repair, and heterochromatin defects exhibited when the protein is overexpressed. The heterologous expression of camelid single-chain antibodies to the nucleosome acidic patch confers a similar range of phenotypes, with the most severe observed when an "arginine-anchor" mode of binding analogous to many endogenous factors is employed. This highlights a delicate balance between nucleosome acidic patch interactors critical for normal cellular function and dysregulated in disease.

PubMed: 42423308
DOI: 10.1093/nar/gkag693

Experimental method

ELECTRON MICROSCOPY (3.17 Å)