8GA8
Structure of the yeast (HDAC) Rpd3L complex
Summary for 8GA8
| Entry DOI | 10.2210/pdb8ga8/pdb |
| EMDB information | 29892 |
| Descriptor | Transcriptional regulatory protein SDS3, Transcriptional regulatory protein SIN3, Transcriptional regulatory protein SAP30, ... (9 entities in total) |
| Functional Keywords | hdac, silencing, chromatin, transcription |
| Biological source | Saccharomyces cerevisiae (baker's yeast) More |
| Total number of polymer chains | 10 |
| Total formula weight | 675551.55 |
| Authors | Patel, A.B.,Radhakrishnan, I.,He, Y. (deposition date: 2023-02-22, release date: 2023-07-12, Last modification date: 2024-06-19) |
| Primary citation | Patel, A.B.,Qing, J.,Tam, K.H.,Zaman, S.,Luiso, M.,Radhakrishnan, I.,He, Y. Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex. Nat Commun, 14:3061-3061, 2023 Cited by PubMed Abstract: The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors. PubMed: 37244892DOI: 10.1038/s41467-023-38687-z PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.5 Å) |
Structure validation
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