View source for 8kd2


==Rpd3S in complex with 187bp nucleosome==
<StructureSection load='8kd2' size='340' side='right'caption='[[8kd2]], [[Resolution|resolution]] 3.02&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8kd2]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae], [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8KD2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8KD2 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.02&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8kd2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8kd2 OCA], [https://pdbe.org/8kd2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8kd2 RCSB], [https://www.ebi.ac.uk/pdbsum/8kd2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8kd2 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RPD3_YEAST RPD3_YEAST] Catalytic component of the RPD3 histone deacetylase (HDAC) complexes RPD3C(L) and RPD3C(S) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation plays an important role in transcriptional regulation, cell cycle progression, DNA damage response, osmotic stress response and developmental events. Is involved in rDNA and telomere silencing and in double strand breaks repair. Required for both full transcription repression and activation of many genes including cell type-specific genes (STE6, TY2 and HO), cell differentiation-specific genes (SPO13), genes that respond to external signals (PHO5) and TRK2. The RPD3 complexes regulate also chromosomal replication timing.<ref>PMID:10079324</ref> <ref>PMID:10359799</ref> <ref>PMID:10388812</ref> <ref>PMID:10931932</ref> <ref>PMID:11069890</ref> <ref>PMID:12089521</ref> <ref>PMID:12192044</ref> <ref>PMID:12808094</ref> <ref>PMID:14711989</ref> <ref>PMID:14737171</ref> <ref>PMID:15141165</ref> <ref>PMID:15143171</ref> <ref>PMID:15456858</ref> <ref>PMID:16286008</ref> <ref>PMID:1944291</ref> <ref>PMID:8962081</ref> <ref>PMID:8978024</ref> <ref>PMID:9512514</ref> <ref>PMID:9710596</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
In Saccharomyces cerevisiae, cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase (HDAC) complex Rpd3S, which is carried by the transcribing RNA polymerase II (RNAPII) to deacetylate and stabilize chromatin. Despite its fundamental importance, the mechanisms by which Rpd3S deacetylates nucleosomes and regulates chromatin dynamics remain elusive. Here, we determined several cryo-EM structures of Rpd3S in complex with nucleosome core particles (NCPs), including the H3/H4 deacetylation states, the alternative deacetylation state, the linker tightening state, and a state in which Rpd3S co-exists with the Hho1 linker histone on NCP. These structures suggest that Rpd3S utilizes a conserved Sin3 basic surface to navigate through the nucleosomal DNA, guided by its interactions with H3K36 methylation and the extra-nucleosomal DNA linkers, to target acetylated H3K9 and sample other histone tails. Furthermore, our structures illustrate that Rpd3S reconfigures the DNA linkers and acts in concert with Hho1 to engage the NCP, potentially unraveling how Rpd3S and Hho1 work in tandem for gene silencing.

Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex.,Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J Cell Res. 2023 Oct;33(10):790-801. doi: 10.1038/s41422-023-00869-1. Epub 2023 Sep , 4. PMID:37666978<ref>PMID:37666978</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8kd2" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Synthetic construct]]
[[Category: Xenopus laevis]]
[[Category: Chao WCH]]
[[Category: Dong S]]
[[Category: Gao X]]
[[Category: Guan J]]
[[Category: He J]]
[[Category: Huang J]]
[[Category: Li H]]
[[Category: Li M]]
[[Category: Li W]]
[[Category: Rasheed N]]
[[Category: Shi X]]
[[Category: Wang C]]
[[Category: Wang M]]
[[Category: Wong KH]]
[[Category: Zhang J]]
[[Category: Zhang X]]
[[Category: Zhang Y]]
[[Category: Zhou M]]
[[Category: Zhou N]]
[[Category: Zou B]]