Structure of human SIRT6 in complex with the nucleosome

a, Front (top) and side (bottom) views of a composite cryo-EM reconstruction of human SIRT6-nucleosome. Maps from focused refinements of SIRT6 (magenta – Rossmann fold and Zn-finger domains labelled) and the nucleosome (H2A – yellow; H2B – orange; H3 – blue; H4 – green; DNA – light and dim grey). b, Corresponding views of the atomic model of the complex.

Flexibility of the SIRT6 Rossmann fold

a, UMAP projection of the latent embeddings of a subset of SIRT6-nucleosome particles representing the concerted movement of the Rossmann fold and the DNA terminus. b, Structural representation of the two endpoints of the latent embeddings shown in panel a. c, Overlay of the DNA ends and the SIRT6 Rossmann fold of two endpoints shown in panel b. Arrows show their displacements between the two endpoints. d, UMAP projection of the latent embeddings of another subset of SIRT6-nucleosome particles representing the movement of the Rossmann fold with respect to the nucleosomal DNA. e, Structural representation of the two endpoints of the latent embeddings shown in panel b. f, Overlay of the DNA ends and the SIRT6 Rossmann fold of two endpoints shown in panel e. Arrow show the displacement of the Rossmann fold between the two endpoints.

Binding of SIRT6 to the nucleosome

a, Close up view on zinc-finger interactions with the acidic patch. Color code as in Fig 1. b, Protein sequence alignment of human sirtuins. Red boxes and asterisks depict the residues of SIRT6 interacting with the acidic patch of the nucleosome. c, Protein sequence alignment of SIRT6 from different species highlighting the same amino acids as in panel b. Organisms: mm Mus musculus, rn Rattus norvegicus, bt Bos taurus, hs Homo sapiens and cc Castor canadensis. d, Depiction of the 3 arginines of SIRT6 (magenta) interacting with the DNA (grey). e, H2A c-terminal tail (yellow) interacts with SIRT6(magenta). f, SIRT6 binding to H2A or H2AZ containing nucleosomes. Bars show the fraction of residual nucleosomes that did not shift with bound SIRT6 in an electron-mobility shift assay (Supplemental Fig. 9). Bars represent mean ± SD of three biological replicates (shown as dots). ** indicates a statistically significant difference between the fraction of residual H2A and H2A.Z containing nucleosomes (P=0.0016 in paired t-test).

SIRT6 poised to deacetylate lysine residues of H3

a, Side View of SIRT6 bound to the nucleosome with histone H3 K9 residue (red sphere) closest to the SIRT6 active site (blue spheres) from a set of molecular dynamics simulations. b, Side View of SIRT6 bound to the nucleosome with histone H3 K18 residue (orange sphere) closest to the SIRT6 active site from a set of molecular dynamics simulations. c, All H3K9 positions (red spheres) in close proximity (<15 Å) to the SIRT6 active site (blue) taken from a set of 15 molecular dynamics simulations and depicted on the surface view of SIRT6 bound to nucleosome. d, All H3K18 positions (orange spheres) in close proximity (<15 Å) to the SIRT6 active site (blue) taken from a set of 15 molecular dynamics simulations and depicted on the surface view of SIRT6 bound to nucleosome. e, Molecular dynamics simulations show that H3 c-terminal tail (blue) can protrude towards SIRT6 in a space formed between the histone octamer and the DNA. H3K27 is shown in red.