7wd3: Difference between revisions

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-'''Unreleased structure'''
-The entry 7wd3 is ON HOLD
+==Cryo-EM structure of Drg1 hexamer treated with ATP and benzo-diazaborine==
+<StructureSection load='7wd3' size='340' side='right'caption='[[7wd3]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7wd3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WD3 FirstGlance]. <br>
+</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=NDT:2-(TOLUENE-4-SULFONYL)-2H-BENZO[D][1,2,3]DIAZABORININ-1-OL'>NDT</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=7wd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wd3 OCA], [https://pdbe.org/7wd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wd3 RCSB], [https://www.ebi.ac.uk/pdbsum/7wd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wd3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A6A5PRU8_YEASX A0A6A5PRU8_YEASX]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The type II AAA + ATPase Drg1 is a ribosome assembly factor, functioning to release Rlp24 from the pre-60S particle just exported from nucleus, and its activity in can be inhibited by a drug molecule diazaborine. However, molecular mechanisms of Drg1-mediated Rlp24 removal and diazaborine-mediated inhibition are not fully understood. Here, we report Drg1 structures in different nucleotide-binding and benzo-diazaborine treated states. Drg1 hexamers transits between two extreme conformations (planar or helical arrangement of protomers). By forming covalent adducts with ATP molecules in both ATPase domain, benzo-diazaborine locks Drg1 hexamers in a symmetric and non-productive conformation to inhibits both inter-protomer and inter-ring communication of Drg1 hexamers. We also obtained a substrate-engaged mutant Drg1 structure, in which conserved pore-loops form a spiral staircase to interact with the polypeptide through a sequence-independent manner. Structure-based mutagenesis data highlight the functional importance of the pore-loop, the D1-D2 linker and the inter-subunit signaling motif of Drg1, which share similar regulatory mechanisms with p97. Our results suggest that Drg1 may function as an unfoldase that threads a substrate protein within the pre-60S particle.
-Authors: Ma, C.Y., Wu, D.M., Chen, Q., Gao, N.
+Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition.,Ma C, Wu D, Chen Q, Gao N Nat Commun. 2022 Nov 9;13(1):6765. doi: 10.1038/s41467-022-34511-2. PMID:36351914<ref>PMID:36351914</ref>
-Description: Cryo-EM structure of Drg1 in the presence of ATP and benzo-diazaborine
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Ma, C.Y]]
+<div class="pdbe-citations 7wd3" style="background-color:#fffaf0;"></div>
-[[Category: Gao, N]]
+== References ==
-[[Category: Chen, Q]]
+<references/>
-[[Category: Wu, D.M]]
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Saccharomyces cerevisiae]]
+[[Category: Chen Q]]
+[[Category: Gao N]]
+[[Category: Ma CY]]
+[[Category: Wu DM]]