8hpo

From Proteopedia

(Difference between revisions)

Revision as of 07:33, 3 May 2023

Cryo-EM structure of a SIN3/HDAC complex from budding yeast

Structural highlights

8hpo is a 11 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UME1_YEAST Catalytic component of the RPD3 histone deacetylase 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 gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.^[1] ^[2] ^[3]

Publication Abstract from PubMed

SIN3-HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM structure of the budding yeast SIN3-HDAC complex Rpd3L at an average resolution of 2.6 A. The structure reveals that two distinct arms (ARM1 and ARM2) hang on a T-shaped scaffold formed by two coiled-coil domains. In each arm, Sin3 interacts with different subunits to create a different environment for the histone deacetylase Rpd3. ARM1 is in the inhibited state with the active site of Rpd3 blocked, whereas ARM2 is in an open conformation with the active site of Rpd3 exposed to the exterior space. The observed asymmetric architecture of Rpd3L is different from those of available structures of other class I HDAC complexes. Our study reveals the organization mechanism of the SIN3-HDAC complex and provides insights into the interaction pattern by which it targets histone deacetylase to chromatin.

Structure of a SIN3-HDAC complex from budding yeast.,Guo Z, Chu C, Lu Y, Zhang X, Xiao Y, Wu M, Gao S, Wong CCL, Zhan X, Wang C Nat Struct Mol Biol. 2023 Apr 20. doi: 10.1038/s41594-023-00975-z. PMID:37081318^[4]

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

References

↑ Mallory MJ, Strich R. Ume1p represses meiotic gene transcription in Saccharomyces cerevisiae through interaction with the histone deacetylase Rpd3p. J Biol Chem. 2003 Nov 7;278(45):44727-34. PMID:12954623 doi:10.1074/jbc.M308632200
↑ Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, Schuldiner M, Chin K, Punna T, Thompson NJ, Boone C, Emili A, Weissman JS, Hughes TR, Strahl BD, Grunstein M, Greenblatt JF, Buratowski S, Krogan NJ. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell. 2005 Nov 18;123(4):593-605. PMID:16286008 doi:10.1016/j.cell.2005.10.025
↑ Pemberton LF, Blobel G. Characterization of the Wtm proteins, a novel family of Saccharomyces cerevisiae transcriptional modulators with roles in meiotic regulation and silencing. Mol Cell Biol. 1997 Aug;17(8):4830-41. PMID:9234739 doi:10.1128/MCB.17.8.4830
↑ Guo Z, Chu C, Lu Y, Zhang X, Xiao Y, Wu M, Gao S, Wong CCL, Zhan X, Wang C. Structure of a SIN3-HDAC complex from budding yeast. Nat Struct Mol Biol. 2023 Apr 20. PMID:37081318 doi:10.1038/s41594-023-00975-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/8hpo"

Categories: Large Structures | Saccharomyces cerevisiae S288C | Guo Z | Wang C | Zhan X

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8hpo is ON HOLD
+==Cryo-EM structure of a SIN3/HDAC complex from budding yeast==
+<StructureSection load='8hpo' size='340' side='right'caption='[[8hpo]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8hpo]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8HPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8HPO FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene>, <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=8hpo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8hpo OCA], [https://pdbe.org/8hpo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8hpo RCSB], [https://www.ebi.ac.uk/pdbsum/8hpo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8hpo ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UME1_YEAST UME1_YEAST] Catalytic component of the RPD3 histone deacetylase 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 gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events.<ref>PMID:12954623</ref> <ref>PMID:16286008</ref> <ref>PMID:9234739</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+SIN3-HDAC (histone deacetylases) complexes have important roles in facilitating local histone deacetylation to regulate chromatin accessibility and gene expression. Here, we present the cryo-EM structure of the budding yeast SIN3-HDAC complex Rpd3L at an average resolution of 2.6 A. The structure reveals that two distinct arms (ARM1 and ARM2) hang on a T-shaped scaffold formed by two coiled-coil domains. In each arm, Sin3 interacts with different subunits to create a different environment for the histone deacetylase Rpd3. ARM1 is in the inhibited state with the active site of Rpd3 blocked, whereas ARM2 is in an open conformation with the active site of Rpd3 exposed to the exterior space. The observed asymmetric architecture of Rpd3L is different from those of available structures of other class I HDAC complexes. Our study reveals the organization mechanism of the SIN3-HDAC complex and provides insights into the interaction pattern by which it targets histone deacetylase to chromatin.
-Authors:
+Structure of a SIN3-HDAC complex from budding yeast.,Guo Z, Chu C, Lu Y, Zhang X, Xiao Y, Wu M, Gao S, Wong CCL, Zhan X, Wang C Nat Struct Mol Biol. 2023 Apr 20. doi: 10.1038/s41594-023-00975-z. PMID:37081318<ref>PMID:37081318</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 8hpo" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Saccharomyces cerevisiae S288C]]
+[[Category: Guo Z]]
+[[Category: Wang C]]
+[[Category: Zhan X]]

8hpo

From Proteopedia

Revision as of 07:33, 3 May 2023

Cryo-EM structure of a SIN3/HDAC complex from budding yeast

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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