8IFG

Cryo-EM structure of the Clr6S (Clr6-HDAC) complex from S. pombe

Summary for 8IFG

• Entry DOI: 10.2210/pdb8ifg/pdb
• EMDB information: 35416 35417 36278
• Descriptor: RbAp48-related WD40 repeat-containing protein prw1, Paired amphipathic helix protein pst2, Histone deacetylase clr6, ... (8 entities in total)
• Functional Keywords: rpd3s, histone deacetylase, hdac, clr6, rpd3, clr6s, clr6 hdac, transcription
• Biological source: Schizosaccharomyces pombe (strain 972 / ATCC 24843); More
• Total number of polymer chains: 7
• Total formula weight: 411810.32

Authors

Zhang, H.Q.,Wang, X.,Wang, Y.N.,Liu, S.M.,Zhang, Y.,Xu, K.,Ji, L.T.,Kornberg, R.D. (deposition date: 2023-02-17, release date: 2024-01-03)

Primary citation

Wang, X.,Wang, Y.,Liu, S.,Zhang, Y.,Xu, K.,Ji, L.,Kornberg, R.D.,Zhang, H.
Class I histone deacetylase complex: Structure and functional correlates.
Proc Natl Acad Sci U S A, 120:e2307598120-, 2023

PubMed Abstract: The Clr6S complex, a class I histone deacetylase complex, functions as a zinc-dependent enzyme to remove acetyl groups from lysine residues in histone tails. We report here the cryo-EM structure of Clr6S alone and a cryo-EM map of Clr6S in complex with a nucleosome. The active center, revealed at near-atomic resolution, includes features important for catalysis-A water molecule coordinated by zinc, the likely nucleophile for attack on the acetyl-lysine bond, and a loop that may position the substrate for catalysis. The cryo-EM map in the presence of a nucleosome reveals multiple Clr6S-nucleosome contacts and a high degree of relative motion of Clr6S and the nucleosome. Such flexibility may be attributed to interaction at a site in the flexible histone tail and is likely important for the function of the deacetylase, which acts at multiple sites in other histone tails.

PubMed: 37459529
DOI: 10.1073/pnas.2307598120

Experimental method

ELECTRON MICROSCOPY (3.2 Å)