8etu

From Proteopedia

(Difference between revisions)

Revision as of 06:13, 19 July 2023

Class2 of the INO80-Hexasome complex

Structural highlights

8etu is a 10 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.
Method:	Electron Microscopy, Resolution 2.8Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RUVB2_YEAST DNA helicase which participates in several chromatin remodeling complexes, including the SWR1 and the INO80 complexes. The SWR1 complex mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. The INO80 complex remodels chromatin by shifting nucleosomes. Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates. The INO80 complex is involved in DNA repair by associating to 'Ser-129' phosphorylated H2A histones as a response to DNA damage. During transcription may recruit SPT15/TBP to the TATA-boxes of involved genes. Required for box C/D and box H/ACA snoRNA accumulation and involved in pre-rRNA processing.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report structures of S. cerevisiae INO80 bound to a hexasome or a nucleosome. INO80 binds the two substrates in substantially different orientations. On a hexasome, INO80 places its ATPase subunit, Ino80, at superhelical location (SHL)-2, across from SHL-6/-7 as previously seen on nucleosomes. Our results suggest that INO80 action on hexasomes resembles action by other remodelers on nucleosomes, such that Ino80 is maximally active near SHL-2. The SHL-2 position also plays a critical role for nucleosome remodeling by INO80. Overall, the mechanistic adaptations used by INO80 for preferential hexasome sliding imply that sub-nucleosomal particles play considerable regulatory roles.

Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility.,Wu H, Munoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y Science. 2023 Jun 28. doi: 10.1126/science.adf4197. PMID:37384669^[10]

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

References

↑ Lim CR, Kimata Y, Ohdate H, Kokubo T, Kikuchi N, Horigome T, Kohno K. The Saccharomyces cerevisiae RuvB-like protein, Tih2p, is required for cell cycle progression and RNA polymerase II-directed transcription. J Biol Chem. 2000 Jul 21;275(29):22409-17. PMID:10787406 doi:http://dx.doi.org/10.1074/jbc.M001031200
↑ Shen X, Mizuguchi G, Hamiche A, Wu C. A chromatin remodelling complex involved in transcription and DNA processing. Nature. 2000 Aug 3;406(6795):541-4. PMID:10952318 doi:http://dx.doi.org/10.1038/35020123
↑ Jonsson ZO, Dhar SK, Narlikar GJ, Auty R, Wagle N, Pellman D, Pratt RE, Kingston R, Dutta A. Rvb1p and Rvb2p are essential components of a chromatin remodeling complex that regulates transcription of over 5% of yeast genes. J Biol Chem. 2001 May 11;276(19):16279-88. Epub 2001 Feb 5. PMID:11278922 doi:http://dx.doi.org/10.1074/jbc.M011523200
↑ King TH, Decatur WA, Bertrand E, Maxwell ES, Fournier MJ. A well-connected and conserved nucleoplasmic helicase is required for production of box C/D and H/ACA snoRNAs and localization of snoRNP proteins. Mol Cell Biol. 2001 Nov;21(22):7731-46. PMID:11604509 doi:http://dx.doi.org/10.1128/MCB.21.22.7731-7746.2001
↑ Ohdate H, Lim CR, Kokubo T, Matsubara K, Kimata Y, Kohno K. Impairment of the DNA binding activity of the TATA-binding protein renders the transcriptional function of Rvb2p/Tih2p, the yeast RuvB-like protein, essential for cell growth. J Biol Chem. 2003 Apr 25;278(17):14647-56. Epub 2003 Feb 6. PMID:12576485 doi:http://dx.doi.org/10.1074/jbc.M213220200
↑ Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science. 2004 Jan 16;303(5656):343-8. Epub 2003 Nov 26. PMID:14645854 doi:10.1126/science.1090701
↑ Krogan NJ, Keogh MC, Datta N, Sawa C, Ryan OW, Ding H, Haw RA, Pootoolal J, Tong A, Canadien V, Richards DP, Wu X, Emili A, Hughes TR, Buratowski S, Greenblatt JF. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell. 2003 Dec;12(6):1565-76. PMID:14690608
↑ Kobor MS, Venkatasubrahmanyam S, Meneghini MD, Gin JW, Jennings JL, Link AJ, Madhani HD, Rine J. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2004 May;2(5):E131. Epub 2004 Mar 23. PMID:15045029 doi:10.1371/journal.pbio.0020131
↑ Jonsson ZO, Jha S, Wohlschlegel JA, Dutta A. Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex. Mol Cell. 2004 Nov 5;16(3):465-77. PMID:15525518 doi:http://dx.doi.org/S1097276504005854
↑ Wu H, Muñoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y. Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility. Science. 2023 Jun 28. PMID:37384669 doi:10.1126/science.adf4197

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/8etu"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8etu is ON HOLD
+==Class2 of the INO80-Hexasome complex==
+<StructureSection load='8etu' size='340' side='right'caption='[[8etu]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8etu]] is a 10 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=8ETU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8ETU 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]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</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=8etu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8etu OCA], [https://pdbe.org/8etu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8etu RCSB], [https://www.ebi.ac.uk/pdbsum/8etu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8etu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RUVB2_YEAST RUVB2_YEAST] DNA helicase which participates in several chromatin remodeling complexes, including the SWR1 and the INO80 complexes. The SWR1 complex mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. The INO80 complex remodels chromatin by shifting nucleosomes. Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates. The INO80 complex is involved in DNA repair by associating to 'Ser-129' phosphorylated H2A histones as a response to DNA damage. During transcription may recruit SPT15/TBP to the TATA-boxes of involved genes. Required for box C/D and box H/ACA snoRNA accumulation and involved in pre-rRNA processing.<ref>PMID:10787406</ref> <ref>PMID:10952318</ref> <ref>PMID:11278922</ref> <ref>PMID:11604509</ref> <ref>PMID:12576485</ref> <ref>PMID:14645854</ref> <ref>PMID:14690608</ref> <ref>PMID:15045029</ref> <ref>PMID:15525518</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report structures of S. cerevisiae INO80 bound to a hexasome or a nucleosome. INO80 binds the two substrates in substantially different orientations. On a hexasome, INO80 places its ATPase subunit, Ino80, at superhelical location (SHL)-2, across from SHL-6/-7 as previously seen on nucleosomes. Our results suggest that INO80 action on hexasomes resembles action by other remodelers on nucleosomes, such that Ino80 is maximally active near SHL-2. The SHL-2 position also plays a critical role for nucleosome remodeling by INO80. Overall, the mechanistic adaptations used by INO80 for preferential hexasome sliding imply that sub-nucleosomal particles play considerable regulatory roles.
-Authors:
+Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility.,Wu H, Munoz EN, Hsieh LJ, Chio US, Gourdet MA, Narlikar GJ, Cheng Y Science. 2023 Jun 28. doi: 10.1126/science.adf4197. PMID:37384669<ref>PMID:37384669</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 8etu" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Saccharomyces cerevisiae S288C]]
+[[Category: Cheng YF]]
+[[Category: Gourdet M]]
+[[Category: Munoz E]]
+[[Category: Narlikar G]]
+[[Category: Wu H]]

8etu

From Proteopedia

Revision as of 06:13, 19 July 2023

Class2 of the INO80-Hexasome complex

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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