View source for 5nbm


==Crystal structure of the Arp4-N-actin(ATP-state) heterodimer bound by a nanobody==
<StructureSection load='5nbm' size='340' side='right'caption='[[5nbm]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5nbm]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C], [https://en.wikipedia.org/wiki/Trichoplusia_ni Trichoplusia ni] and [https://en.wikipedia.org/wiki/Vicugna_pacos Vicugna pacos]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NBM FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HIC:4-METHYL-HISTIDINE'>HIC</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=5nbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nbm OCA], [https://pdbe.org/5nbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nbm RCSB], [https://www.ebi.ac.uk/pdbsum/5nbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nbm ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ARP4_YEAST ARP4_YEAST] Chromatin interaction component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. ARP4 recognizes H2AS128ph (gamma-H2A) and is required for NuA4 complex integrity. Component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the INO80 complex which 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 gamma-H2A as a response to DNA damage.<ref>PMID:10911987</ref> <ref>PMID:10952318</ref> <ref>PMID:11937627</ref> <ref>PMID:12353039</ref> <ref>PMID:14622406</ref> <ref>PMID:14645854</ref> <ref>PMID:14690608</ref> <ref>PMID:15045029</ref> <ref>PMID:15610740</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Nuclear actin (N-actin) and actin-related proteins (Arps) are critical components of several chromatin modulating complexes, including the chromatin remodeler INO80, but their function is largely elusive. Here, we report the crystal structure of the 180-kDa Arp8 module of Saccharomyces cerevisiae INO80 and establish its role in recognition of extranucleosomal linker DNA. Arp8 engages N-actin in a manner distinct from that of other actin-fold proteins and thereby specifies recruitment of the Arp4-N-actin heterodimer to a segmented scaffold of the helicase-SANT-associated (HSA) domain of Ino80. The helical HSA domain spans over 120 A and provides an extended binding platform for extranucleosomal entry DNA that is required for nucleosome sliding and genome-wide nucleosome positioning. Together with the recent cryo-electron microscopy structure of INO80(Core)-nucleosome complex, our findings suggest an allosteric mechanism by which INO80 senses 40-bp linker DNA to conduct highly processive chromatin remodeling.

The nuclear actin-containing Arp8 module is a linker DNA sensor driving INO80 chromatin remodeling.,Knoll KR, Eustermann S, Niebauer V, Oberbeckmann E, Stoehr G, Schall K, Tosi A, Schwarz M, Buchfellner A, Korber P, Hopfner KP Nat Struct Mol Biol. 2018 Sep;25(9):823-832. doi: 10.1038/s41594-018-0115-8. Epub, 2018 Sep 3. PMID:30177756<ref>PMID:30177756</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5nbm" style="background-color:#fffaf0;"></div>

==See Also==
*[[Actin-related protein 3D structures|Actin-related protein 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Trichoplusia ni]]
[[Category: Vicugna pacos]]
[[Category: Eustermann S]]
[[Category: Hopfner KP]]
[[Category: Knoll KR]]