Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
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Journal
IF	>30 >20 >10 >5 all

Title	Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition.
Journal, issue, pages	Nat Commun, Vol. 13, Issue 1, Page 6765, Year 2022
Publish date	Nov 9, 2022
Authors	Chengying Ma / Damu Wu / Qian Chen / Ning Gao /
PubMed Abstract	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 ...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.
External links	Nat Commun / PubMed:36351914 / PubMed Central
Methods	EM (single particle)
Resolution	3.6 - 5.9 Å
Structure data	32396 7wbb EMDB-32396, PDB-7wbb: Cryo-EM structure of substrate engaged Drg1 hexamer Method: EM (single particle) / Resolution: 3.6 Å 32397 7ykk EMDB-32397: The Cryo-EM structure of Drg1 hexamer treated with ADP PDB-7ykk: Cryo-EM structure of Drg1 hexamer treated with ADP Method: EM (single particle) / Resolution: 5.9 Å 32399 7ykl EMDB-32399: The Cryo-EM structure of Drg1 hexamer treated with AMPPNP PDB-7ykl: Cryo-EM structure of Drg1 hexamer treated with AMPPNP Method: EM (single particle) / Resolution: 5.6 Å 32400 7ykt EMDB-32400: The Cryo-EM structure of Drg1 hexamer in helical state treated with ADP/AMPPNP/benzo-diazaborine PDB-7ykt: Cryo-EM structure of Drg1 hexamer in helical state treated with ADP/AMPPNP/benzo-diazaborine Method: EM (single particle) / Resolution: 5.9 Å 32402 7ykz EMDB-32402: The Cryo-EM structure of Drg1 hexamer in planar state treated with ADP/AMPPNP/benzo-diazaborine PDB-7ykz: Cryo-EM structure of Drg1 hexamer in the planar state treated with ADP/AMPPNP/Diazaborine Method: EM (single particle) / Resolution: 4.3 Å 32403 7wd3 EMDB-32403: Cryo-EM structure of Drg1 hexamer treated with ATP/benzo-diazaborine PDB-7wd3: Cryo-EM structure of Drg1 hexamer treated with ATP and benzo-diazaborine Method: EM (single particle) / Resolution: 3.8 Å
Chemicals	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM / Adenosine triphosphate ChemComp-NDT: 2-(TOLUENE-4-SULFONYL)-2H-BENZO[D][1,2,3]DIAZABORININ-1-OL ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate
Source	saccharomyces cerevisiae (brewer's yeast) escherichia coli (E. coli)
Keywords	ATP-binding protein / cryo-EM structure of Drg1 / RIBOSOME / Drg1 / RIBOSOMAL PROTEIN / Involved in maturation of pre-60S ribosomal particles