7wd3

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(New page: '''Unreleased structure''' The entry 7wd3 is ON HOLD Authors: Ma, C.Y., Wu, D.M., Chen, Q., Gao, N. Description: Cryo-EM structure of Drg1 in the presence of ATP/diazaborine [[Category...)
Current revision (06:20, 3 July 2025) (edit) (undo)
 
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'''Unreleased structure'''
 
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The entry 7wd3 is ON HOLD
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==Cryo-EM structure of Drg1 hexamer treated with ATP and benzo-diazaborine==
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<StructureSection load='7wd3' size='340' side='right'caption='[[7wd3]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
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<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>
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/AFG2_YEAST AFG2_YEAST] ATP-dependent chaperone which uses the energy provided by ATP hydrolysis to generate mechanical force to disassemble protein complexes (PubMed:12006565, PubMed:17646390, PubMed:23185031, PubMed:24371142). Plays an essential role in the cytoplasmic maturation steps of pre-60S ribosomal particles by promoting the release of shuttling protein RLP24 from the pre-ribosomal particles (PubMed:17646390, PubMed:23185031, PubMed:24371142). This step facilitates the subsequent release of other shuttling proteins such as NOG1 and allows the transition of the pre-ribosomal particles to later maturation forms that bind REI1 (PubMed:17646390, PubMed:23185031, PubMed:24371142). Essential for viability (PubMed:24371142, PubMed:8109176).<ref>PMID:12006565</ref> <ref>PMID:17646390</ref> <ref>PMID:23185031</ref> <ref>PMID:24371142</ref> <ref>PMID:8109176</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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Authors: Ma, C.Y., Wu, D.M., Chen, Q., Gao, N.
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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>
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Description: Cryo-EM structure of Drg1 in the presence of ATP/diazaborine
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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[[Category: Ma, C.Y]]
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<div class="pdbe-citations 7wd3" style="background-color:#fffaf0;"></div>
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[[Category: Gao, N]]
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== References ==
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[[Category: Chen, Q]]
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<references/>
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[[Category: Wu, D.M]]
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Saccharomyces cerevisiae]]
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[[Category: Chen Q]]
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[[Category: Gao N]]
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[[Category: Ma CY]]
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[[Category: Wu DM]]

Current revision

Cryo-EM structure of Drg1 hexamer treated with ATP and benzo-diazaborine

PDB ID 7wd3

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