9ob1: Difference between revisions

Latest revision as of 07:51, 4 March 2026

S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State

Structural highlights

9ob1 is a 16 chain structure with sequence from Saccharomyces cerevisiae and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.2Å
Ligands:	ADP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RUVB1_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. RVB1 recruits ARP5 to the INO80 complex. 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]

Publication Abstract from PubMed

Increasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like activity. Using cryogenic electron microscopy, we show that on nucleosomes with 40 bp of flanking DNA, the Arp8 module rotates 180 degrees away from the DNA. Deleting the Arp8 module enables rapid sliding irrespective of flanking DNA length. Thus, rather than enabling a ruler-like activity, the Arp8 module acts as a brake on INO80 remodeling when flanking DNA is short. This autoinhibition-based mechanism has broad implications for understanding how primitive nucleosome mobilization enzymes may have evolved into sophisticated remodelers.

Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning.,Kaur U, Wu H, Cheng Y, Narlikar GJ Science. 2025 Jul 17;389(6757):eadr3831. doi: 10.1126/science.adr3831. Epub 2025 , Jul 17. PMID:40674492^[7]

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

References

↑ 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:https://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:https://dx.doi.org/10.1074/jbc.M011523200
↑ 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:https://dx.doi.org/S1097276504005854
↑ Kaur U, Wu H, Cheng Y, Narlikar GJ. Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning. Science. 2025 Jul 17;389(6757):eadr3831. PMID:40674492 doi:10.1126/science.adr3831

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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:https://dx.doi.org/10.1038/35020123

[2] 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:https://dx.doi.org/10.1074/jbc.M011523200

[3] 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

[4] 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

[5] 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

[6] 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:https://dx.doi.org/S1097276504005854

[7] Kaur U, Wu H, Cheng Y, Narlikar GJ. Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning. Science. 2025 Jul 17;389(6757):eadr3831. PMID:40674492 doi:10.1126/science.adr3831

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[2]

[3]

[4]

[5]

[6]

[7]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9ob1 is ON HOLD  until Paper Publication
+==S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State==
+<StructureSection load='9ob1' size='340' side='right'caption='[[9ob1]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9ob1]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] 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=9OB1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9OB1 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]] 3.2&#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=9ob1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ob1 OCA], [https://pdbe.org/9ob1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ob1 RCSB], [https://www.ebi.ac.uk/pdbsum/9ob1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ob1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RUVB1_YEAST RUVB1_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. RVB1 recruits ARP5 to the INO80 complex. 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:10952318</ref> <ref>PMID:11278922</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 ==
+Increasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like activity. Using cryogenic electron microscopy, we show that on nucleosomes with 40 bp of flanking DNA, the Arp8 module rotates 180 degrees away from the DNA. Deleting the Arp8 module enables rapid sliding irrespective of flanking DNA length. Thus, rather than enabling a ruler-like activity, the Arp8 module acts as a brake on INO80 remodeling when flanking DNA is short. This autoinhibition-based mechanism has broad implications for understanding how primitive nucleosome mobilization enzymes may have evolved into sophisticated remodelers.
-Authors:
+Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning.,Kaur U, Wu H, Cheng Y, Narlikar GJ Science. 2025 Jul 17;389(6757):eadr3831. doi: 10.1126/science.adr3831. Epub 2025 , Jul 17. PMID:40674492<ref>PMID:40674492</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 9ob1" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Saccharomyces cerevisiae]]
+[[Category: Synthetic construct]]
+[[Category: Cheng YF]]
+[[Category: Kaur U]]
+[[Category: Narlikar GJ]]
+[[Category: Wu H]]

9ob1: Difference between revisions

Latest revision as of 07:51, 4 March 2026

S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State

Structural highlights

Function

Publication Abstract from PubMed

References

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