8w9d

From Proteopedia

(Difference between revisions)

Revision as of 05:26, 15 May 2024

Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1

Structural highlights

8w9d is a 17 chain structure with sequence from Homo sapiens and Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.9Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SIN3_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. SIN3 has also a RPD3 independent function required for normal longevity.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18]

Publication Abstract from PubMed

The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron microscopy structures of the budding yeast Rpd3S complex in both its apo and three nucleosome-bound states at atomic resolutions, revealing the exquisite architecture of Rpd3S to well accommodate a mononucleosome without linker DNA. The Rpd3S core, containing a Sin3 Lobe and two NB modules, is a rigid complex and provides three positive-charged anchors (Sin3_HCR and two Rco1_NIDs) to connect nucleosomal DNA. In three nucleosome-bound states, the Rpd3S core exhibits three distinct orientations relative to the nucleosome, assisting the sector-shaped deacetylase Rpd3 to locate above the SHL5-6, SHL0-1, or SHL2-3, respectively. Our work provides a structural framework that reveals a dynamic working model for the Rpd3S complex to engage diverse deacetylation sites.

Structures and dynamics of Rpd3S complex bound to nucleosome.,Wang C, Chu C, Guo Z, Zhan X Sci Adv. 2024 Apr 12;10(15):eadk7678. doi: 10.1126/sciadv.adk7678. Epub 2024 Apr , 10. PMID:38598631^[19]

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

References

↑ Sun ZW, Hampsey M. A general requirement for the Sin3-Rpd3 histone deacetylase complex in regulating silencing in Saccharomyces cerevisiae. Genetics. 1999 Jul;152(3):921-32. PMID:10388812 doi:10.1093/genetics/152.3.921
↑ Elkhaimi M, Kaadige MR, Kamath D, Jackson JC, Biliran H Jr, Lopes JM. Combinatorial regulation of phospholipid biosynthetic gene expression by the UME6, SIN3 and RPD3 genes. Nucleic Acids Res. 2000 Aug 15;28(16):3160-7. PMID:10931932 doi:10.1093/nar/28.16.3160
↑ Washburn BK, Esposito RE. Identification of the Sin3-binding site in Ume6 defines a two-step process for conversion of Ume6 from a transcriptional repressor to an activator in yeast. Mol Cell Biol. 2001 Mar;21(6):2057-69. PMID:11238941 doi:10.1128/MCB.21.6.2057-2069.2001
↑ Scott KL, Plon SE. Loss of Sin3/Rpd3 histone deacetylase restores the DNA damage response in checkpoint-deficient strains of Saccharomyces cerevisiae. Mol Cell Biol. 2003 Jul;23(13):4522-31. PMID:12808094 doi:10.1128/MCB.23.13.4522-4531.2003
↑ Jazayeri A, McAinsh AD, Jackson SP. Saccharomyces cerevisiae Sin3p facilitates DNA double-strand break repair. Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1644-9. PMID:14711989 doi:10.1073/pnas.0304797101
↑ De Nadal E, Zapater M, Alepuz PM, Sumoy L, Mas G, Posas F. The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes. Nature. 2004 Jan 22;427(6972):370-4. PMID:14737171 doi:10.1038/nature02258
↑ Schröder M, Clark R, Liu CY, Kaufman RJ. The unfolded protein response represses differentiation through the RPD3-SIN3 histone deacetylase. EMBO J. 2004 Jun 2;23(11):2281-92. PMID:15141165 doi:10.1038/sj.emboj.7600233
↑ Aparicio JG, Viggiani CJ, Gibson DG, Aparicio OM. The Rpd3-Sin3 histone deacetylase regulates replication timing and enables intra-S origin control in Saccharomyces cerevisiae. Mol Cell Biol. 2004 Jun;24(11):4769-80. PMID:15143171 doi:10.1128/MCB.24.11.4769-4780.2004
↑ Kaeberlein M, Kirkland KT, Fields S, Kennedy BK. Genes determining yeast replicative life span in a long-lived genetic background. Mech Ageing Dev. 2005 Apr;126(4):491-504. PMID:15722108 doi:10.1016/j.mad.2004.10.007
↑ Yoshimoto H, Ohmae M, Yamashita I. The Saccharomyces cerevisiae GAM2/SIN3 protein plays a role in both activation and repression of transcription. Mol Gen Genet. 1992 May;233(1-2):327-30. PMID:1603074 doi:10.1007/BF00587597
↑ 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
↑ Vidal M, Strich R, Esposito RE, Gaber RF. RPD1 (SIN3/UME4) is required for maximal activation and repression of diverse yeast genes. Mol Cell Biol. 1991 Dec;11(12):6306-16. PMID:1944290 doi:10.1128/mcb.11.12.6306-6316.1991
↑ Wang H, Clark I, Nicholson PR, Herskowitz I, Stillman DJ. The Saccharomyces cerevisiae SIN3 gene, a negative regulator of HO, contains four paired amphipathic helix motifs. Mol Cell Biol. 1990 Nov;10(11):5927-36. PMID:2233725 doi:10.1128/mcb.10.11.5927-5936.1990
↑ Wang H, Stillman DJ. Transcriptional repression in Saccharomyces cerevisiae by a SIN3-LexA fusion protein. Mol Cell Biol. 1993 Mar;13(3):1805-14. PMID:8441414 doi:10.1128/mcb.13.3.1805-1814.1993
↑ 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
↑ Kasten MM, Dorland S, Stillman DJ. A large protein complex containing the yeast Sin3p and Rpd3p transcriptional regulators. Mol Cell Biol. 1997 Aug;17(8):4852-8. PMID:9234741 doi:10.1128/MCB.17.8.4852
↑ Rundlett SE, Carmen AA, Suka N, Turner BM, Grunstein M. Transcriptional repression by UME6 involves deacetylation of lysine 5 of histone H4 by RPD3. Nature. 1998 Apr 23;392(6678):831-5. PMID:9572144 doi:10.1038/33952
↑ Kadosh D, Struhl K. Targeted recruitment of the Sin3-Rpd3 histone deacetylase complex generates a highly localized domain of repressed chromatin in vivo. Mol Cell Biol. 1998 Sep;18(9):5121-7. PMID:9710596 doi:10.1128/MCB.18.9.5121
↑ Wang C, Chu C, Guo Z, Zhan X. Structures and dynamics of Rpd3S complex bound to nucleosome. Sci Adv. 2024 Apr 12;10(15):eadk7678. PMID:38598631 doi:10.1126/sciadv.adk7678

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/8w9d"

Categories: Homo sapiens | Large Structures | Saccharomyces cerevisiae | Wang C | Zhan X

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8w9d is ON HOLD  until Paper Publication
+==Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1==
+<StructureSection load='8w9d' size='340' side='right'caption='[[8w9d]], [[Resolution|resolution]] 3.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8w9d]] is a 17 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8W9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8W9D 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]] 3.9&#8491;</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=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=8w9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8w9d OCA], [https://pdbe.org/8w9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8w9d RCSB], [https://www.ebi.ac.uk/pdbsum/8w9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8w9d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SIN3_YEAST SIN3_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. SIN3 has also a RPD3 independent function required for normal longevity.<ref>PMID:10388812</ref> <ref>PMID:10931932</ref> <ref>PMID:11238941</ref> <ref>PMID:12808094</ref> <ref>PMID:14711989</ref> <ref>PMID:14737171</ref> <ref>PMID:15141165</ref> <ref>PMID:15143171</ref> <ref>PMID:15722108</ref> <ref>PMID:1603074</ref> <ref>PMID:16286008</ref> <ref>PMID:1944290</ref> <ref>PMID:2233725</ref> <ref>PMID:8441414</ref> <ref>PMID:8978024</ref> <ref>PMID:9234741</ref> <ref>PMID:9572144</ref> <ref>PMID:9710596</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The Rpd3S complex plays a pivotal role in facilitating local histone deacetylation in the transcribed regions to suppress intragenic transcription initiation. Here, we present the cryo-electron microscopy structures of the budding yeast Rpd3S complex in both its apo and three nucleosome-bound states at atomic resolutions, revealing the exquisite architecture of Rpd3S to well accommodate a mononucleosome without linker DNA. The Rpd3S core, containing a Sin3 Lobe and two NB modules, is a rigid complex and provides three positive-charged anchors (Sin3_HCR and two Rco1_NIDs) to connect nucleosomal DNA. In three nucleosome-bound states, the Rpd3S core exhibits three distinct orientations relative to the nucleosome, assisting the sector-shaped deacetylase Rpd3 to locate above the SHL5-6, SHL0-1, or SHL2-3, respectively. Our work provides a structural framework that reveals a dynamic working model for the Rpd3S complex to engage diverse deacetylation sites.
-Authors:
+Structures and dynamics of Rpd3S complex bound to nucleosome.,Wang C, Chu C, Guo Z, Zhan X Sci Adv. 2024 Apr 12;10(15):eadk7678. doi: 10.1126/sciadv.adk7678. Epub 2024 Apr , 10. PMID:38598631<ref>PMID:38598631</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 8w9d" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Saccharomyces cerevisiae]]
+[[Category: Wang C]]
+[[Category: Zhan X]]

8w9d

From Proteopedia

Revision as of 05:26, 15 May 2024

Cryo-EM structure of the Rpd3S-nucleosome complex from budding yeast in State 1

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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