+Open data
-Basic information
Entry | Database: PDB / ID: 7nku | ||||||
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Title | diazaborine bound Drg1(AFG2) | ||||||
Components | ATPase family gene 2 protein | ||||||
Keywords | RIBOSOME / DRG1 / AFG2 / ribosome maturation / AAA protein / diazaborine / inhibitor | ||||||
Function / homology | Function and homology information mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / protein hexamerization / retrograde protein transport, ER to cytosol / non-chaperonin molecular chaperone ATPase / preribosome, large subunit precursor / autophagosome maturation / polyubiquitin modification-dependent protein binding / ribosomal large subunit biogenesis / response to xenobiotic stimulus ...mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / protein hexamerization / retrograde protein transport, ER to cytosol / non-chaperonin molecular chaperone ATPase / preribosome, large subunit precursor / autophagosome maturation / polyubiquitin modification-dependent protein binding / ribosomal large subunit biogenesis / response to xenobiotic stimulus / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Prattes, M. / Bergler, H. / Haselbach, D. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Authors: Michael Prattes / Irina Grishkovskaya / Victor-Valentin Hodirnau / Ingrid Rössler / Isabella Klein / Christina Hetzmannseder / Gertrude Zisser / Christian C Gruber / Karl Gruber / David ...Authors: Michael Prattes / Irina Grishkovskaya / Victor-Valentin Hodirnau / Ingrid Rössler / Isabella Klein / Christina Hetzmannseder / Gertrude Zisser / Christian C Gruber / Karl Gruber / David Haselbach / Helmut Bergler / Abstract: The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. ...The hexameric AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis and initiates cytoplasmic maturation of the large ribosomal subunit by releasing the shuttling maturation factor Rlp24. Drg1 monomers contain two AAA-domains (D1 and D2) that act in a concerted manner. Rlp24 release is inhibited by the drug diazaborine which blocks ATP hydrolysis in D2. The mode of inhibition was unknown. Here we show the first cryo-EM structure of Drg1 revealing the inhibitory mechanism. Diazaborine forms a covalent bond to the 2'-OH of the nucleotide in D2, explaining its specificity for this site. As a consequence, the D2 domain is locked in a rigid, inactive state, stalling the whole Drg1 hexamer. Resistance mechanisms identified include abolished drug binding and altered positioning of the nucleotide. Our results suggest nucleotide-modifying compounds as potential novel inhibitors for AAA-ATPases. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7nku.cif.gz | 553.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nku.ent.gz | 469.3 KB | Display | PDB format |
PDBx/mmJSON format | 7nku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nku_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7nku_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7nku_validation.xml.gz | 97 KB | Display | |
Data in CIF | 7nku_validation.cif.gz | 141.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/7nku ftp://data.pdbj.org/pub/pdb/validation_reports/nk/7nku | HTTPS FTP |
-Related structure data
Related structure data | 12448MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10717 (Title: Single particle Data of diazaborine bound Drg1 / Data size: 1.6 TB Data #1: Unaligned Multiframe micrographs of DRG1 bound to diazaborine. [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 84850.719 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: AFG2, DRG1, YLR397C, L8084.16 / Production host: Escherichia coli (E. coli) References: UniProt: P32794, non-chaperonin molecular chaperone ATPase #2: Chemical | ChemComp-AGS / #3: Chemical | ChemComp-TDB / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Drg1 (AFG2) bound to diazaborine / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.6 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1152861 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 237914 / Algorithm: FOURIER SPACE / Details: polished with deepenhancer / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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