EMD-16845

Single-particle
2.94 Å
EMD-16845 Deposition: 13/03/2023
Map released: 09/08/2023
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-16845

Nucleosome Bound human SIRT6 (composite structure)

EMD-16845

Single-particle
2.94 Å
EMD-16845 Deposition: 13/03/2023
Map released: 09/08/2023
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Sample Organism: Xenopus laevis, Homo sapiens
Sample: Human Sirtuin 6 in complex with the nucleosome
Fitted models: 8of4 (Avg. Q-score: 0.446)

Deposition Authors: Smirnova E, Bignon E , Schultz P , Papai G , Ben-Shem A
Binding to nucleosome poises human SIRT6 for histone H3 deacetylation.
Smirnova E, Bignon E , Schultz P , Papai G , Ben Shem A
(2024) eLife , 12
PUBMED: 38415718
DOI: doi:10.7554/eLife.87989
ISSN: 2050-084X
Abstract:
Sirtuin 6 (SIRT6) is an NAD+-dependent histone H3 deacetylase that is prominently found associated with chromatin, attenuates transcriptionally active promoters and regulates DNA repair, metabolic homeostasis and lifespan. Unlike other sirtuins, it has low affinity to free histone tails but demonstrates strong binding to nucleosomes. It is poorly understood how SIRT6 docking on nucleosomes stimulates its histone deacetylation activity. Here, we present the structure of human SIRT6 bound to a nucleosome determined by cryogenic electron microscopy. The zinc finger domain of SIRT6 associates tightly with the acidic patch of the nucleosome through multiple arginine anchors. The Rossmann fold domain binds to the terminus of the looser DNA half of the nucleosome, detaching two turns of the DNA from the histone octamer and placing the NAD+ binding pocket close to the DNA exit site. This domain shows flexibility with respect to the fixed zinc finger and moves with, but also relative to, the unwrapped DNA terminus. We apply molecular dynamics simulations of the histone tails in the nucleosome to show that in this mode of interaction, the active site of SIRT6 is perfectly poised to catalyze deacetylation of the H3 histone tail and that the partial unwrapping of the DNA allows even lysines close to the H3 core to reach the enzyme.