8a5o: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[8a5o]] is a 5 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=8A5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5O FirstGlance]. <br>
<table><tr><td colspan='2'>[[8a5o]] is a 5 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=8A5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8A5O FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
</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=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=8a5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5o OCA], [https://pdbe.org/8a5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5o RCSB], [https://www.ebi.ac.uk/pdbsum/8a5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5o ProSAT]</span></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=8a5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8a5o OCA], [https://pdbe.org/8a5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8a5o RCSB], [https://www.ebi.ac.uk/pdbsum/8a5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8a5o ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/INO80_YEAST INO80_YEAST] ATPase component of the INO80 complex which remodels chromatin by shifting nucleosomes and is involved in DNA repair (PubMed:10952318, PubMed:12887900). Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates (PubMed:10952318, PubMed:10361278). The INO80 complex is involved in DNA repair by associating with 'Ser-129' phosphorylated H2A histones as a response to DNA damage (PubMed:15607974, PubMed:15607975).<ref>PMID:10361278</ref> <ref>PMID:10952318</ref> <ref>PMID:12887900</ref> <ref>PMID:15607974</ref> <ref>PMID:15607975</ref>  
[https://www.uniprot.org/uniprot/INO80_YEAST INO80_YEAST] ATPase component of the INO80 complex which remodels chromatin by shifting nucleosomes and is involved in DNA repair (PubMed:10952318, PubMed:12887900). Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates (PubMed:10952318, PubMed:10361278). The INO80 complex is involved in DNA repair by associating with 'Ser-129' phosphorylated H2A histones as a response to DNA damage (PubMed:15607974, PubMed:15607975).<ref>PMID:10361278</ref> <ref>PMID:10952318</ref> <ref>PMID:12887900</ref> <ref>PMID:15607974</ref> <ref>PMID:15607975</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.
Structural mechanism of extranucleosomal DNA readout by the INO80 complex.,Kunert F, Metzner FJ, Jung J, Hopfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S, Hopfner KP Sci Adv. 2022 Dec 9;8(49):eadd3189. doi: 10.1126/sciadv.add3189. Epub 2022 Dec 9. PMID:36490333<ref>PMID:36490333</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8a5o" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 09:43, 24 July 2024

Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80

Structural highlights

8a5o is a 5 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 3.2Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

INO80_YEAST ATPase component of the INO80 complex which remodels chromatin by shifting nucleosomes and is involved in DNA repair (PubMed:10952318, PubMed:12887900). Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates (PubMed:10952318, PubMed:10361278). The INO80 complex is involved in DNA repair by associating with 'Ser-129' phosphorylated H2A histones as a response to DNA damage (PubMed:15607974, PubMed:15607975).[1] [2] [3] [4] [5]

Publication Abstract from PubMed

The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.

Structural mechanism of extranucleosomal DNA readout by the INO80 complex.,Kunert F, Metzner FJ, Jung J, Hopfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S, Hopfner KP Sci Adv. 2022 Dec 9;8(49):eadd3189. doi: 10.1126/sciadv.add3189. Epub 2022 Dec 9. PMID:36490333[6]

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

References

  1. ↑ Ebbert R, Birkmann A, Schuller HJ. The product of the SNF2/SWI2 paralogue INO80 of Saccharomyces cerevisiae required for efficient expression of various yeast structural genes is part of a high-molecular-weight protein complex. Mol Microbiol. 1999 May;32(4):741-51. PMID:10361278
  2. ↑ 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
  3. ↑ Shen X, Ranallo R, Choi E, Wu C. Involvement of actin-related proteins in ATP-dependent chromatin remodeling. Mol Cell. 2003 Jul;12(1):147-55. PMID:12887900
  4. ↑ Morrison AJ, Highland J, Krogan NJ, Arbel-Eden A, Greenblatt JF, Haber JE, Shen X. INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair. Cell. 2004 Dec 17;119(6):767-75. doi: 10.1016/j.cell.2004.11.037. PMID:15607974 doi:http://dx.doi.org/10.1016/j.cell.2004.11.037
  5. ↑ van Attikum H, Fritsch O, Hohn B, Gasser SM. Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair. Cell. 2004 Dec 17;119(6):777-88. doi: 10.1016/j.cell.2004.11.033. PMID:15607975 doi:http://dx.doi.org/10.1016/j.cell.2004.11.033
  6. ↑ Kunert F, Metzner FJ, Jung J, Hopfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S, Hopfner KP. Structural mechanism of extranucleosomal DNA readout by the INO80 complex. Sci Adv. 2022 Dec 9;8(49):eadd3189. doi: 10.1126/sciadv.add3189. Epub 2022 Dec 9. PMID:36490333 doi:http://dx.doi.org/10.1126/sciadv.add3189

8a5o, resolution 3.20Å

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