8ga8

From Proteopedia

(Difference between revisions)

Revision as of 07:23, 12 July 2023

Structure of the yeast (HDAC) Rpd3L complex

Structural highlights

8ga8 is a 10 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.5Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SDS3_YEAST Component of the RPD3C(L) histone deacetylase complex (HDAC) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. SDS3 is required for the HDAC activity of the complex and for the RPD3-SIN3 association.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

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.

Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex.,Patel AB, Qing J, Tam KH, Zaman S, Luiso M, Radhakrishnan I, He Y Nat Commun. 2023 May 27;14(1):3061. doi: 10.1038/s41467-023-38687-z. PMID:37244892^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Dorland S, Deegenaars ML, Stillman DJ. Roles for the Saccharomyces cerevisiae SDS3, CBK1 and HYM1 genes in transcriptional repression by SIN3. Genetics. 2000 Feb;154(2):573-86. PMID:10655212 doi:10.1093/genetics/154.2.573
↑ Lechner T, Carrozza MJ, Yu Y, Grant PA, Eberharter A, Vannier D, Brosch G, Stillman DJ, Shore D, Workman JL. Sds3 (suppressor of defective silencing 3) is an integral component of the yeast Sin3[middle dot]Rpd3 histone deacetylase complex and is required for histone deacetylase activity. J Biol Chem. 2000 Dec 29;275(52):40961-6. PMID:11024051 doi:10.1074/jbc.M005730200
↑ Vannier D, Damay P, Shore D. A role for Sds3p, a component of the Rpd3p/Sin3p deacetylase complex, in maintaining cellular integrity in Saccharomyces cerevisiae. Mol Genet Genomics. 2001 May;265(3):560-8. PMID:11405640 doi:10.1007/s004380100447
↑ Vannier D, Balderes D, Shore D. Evidence that the transcriptional regulators SIN3 and RPD3, and a novel gene (SDS3) with similar functions, are involved in transcriptional silencing in S. cerevisiae. Genetics. 1996 Dec;144(4):1343-53. PMID:8978024 doi:10.1093/genetics/144.4.1343
↑ Patel AB, Qing J, Tam KH, Zaman S, Luiso M, Radhakrishnan I, He Y. Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex. Nat Commun. 2023 May 27;14(1):3061. PMID:37244892 doi:10.1038/s41467-023-38687-z

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8ga8"

Categories: Large Structures | Saccharomyces cerevisiae | He Y | Patel AB | Radhakrishnan I

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8ga8 is ON HOLD
+==Structure of the yeast (HDAC) Rpd3L complex==
+<StructureSection load='8ga8' size='340' side='right'caption='[[8ga8]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8ga8]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8GA8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8GA8 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]] 3.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=8ga8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ga8 OCA], [https://pdbe.org/8ga8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ga8 RCSB], [https://www.ebi.ac.uk/pdbsum/8ga8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ga8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SDS3_YEAST SDS3_YEAST] Component of the RPD3C(L) histone deacetylase complex (HDAC) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. SDS3 is required for the HDAC activity of the complex and for the RPD3-SIN3 association.<ref>PMID:10655212</ref> <ref>PMID:11024051</ref> <ref>PMID:11405640</ref> <ref>PMID:8978024</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-Authors:
+Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex.,Patel AB, Qing J, Tam KH, Zaman S, Luiso M, Radhakrishnan I, He Y Nat Commun. 2023 May 27;14(1):3061. doi: 10.1038/s41467-023-38687-z. PMID:37244892<ref>PMID:37244892</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8ga8" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Saccharomyces cerevisiae]]
+[[Category: He Y]]
+[[Category: Patel AB]]
+[[Category: Radhakrishnan I]]

8ga8

From Proteopedia

Revision as of 07:23, 12 July 2023

Structure of the yeast (HDAC) Rpd3L complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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