+Open data
-Basic information
Entry | Database: PDB / ID: 7z11 | ||||||
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Title | Structure of substrate bound DRG1 (AFG2) | ||||||
Components |
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Keywords | CHAPERONE / Ribosome biogenesis / AAA-ATPases / substrate recognition / single particle cryo-EM | ||||||
Function / homology | Function and homology information protein hexamerization / non-chaperonin molecular chaperone ATPase / preribosome, large subunit precursor / ribosomal large subunit biogenesis / response to xenobiotic stimulus / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Prattes, M. / Grishkovskaya, I. / Bergler, H. / Haselbach, D. | ||||||
Funding support | Austria, 1items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Authors: Michael Prattes / Irina Grishkovskaya / Victor-Valentin Hodirnau / Christina Hetzmannseder / Gertrude Zisser / Carolin Sailer / Vasileios Kargas / Mathias Loibl / Magdalena Gerhalter / Lisa ...Authors: Michael Prattes / Irina Grishkovskaya / Victor-Valentin Hodirnau / Christina Hetzmannseder / Gertrude Zisser / Carolin Sailer / Vasileios Kargas / Mathias Loibl / Magdalena Gerhalter / Lisa Kofler / Alan J Warren / Florian Stengel / David Haselbach / Helmut Bergler / Abstract: The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from ...The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z11.cif.gz | 722.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z11.ent.gz | 608.1 KB | Display | PDB format |
PDBx/mmJSON format | 7z11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z11_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7z11_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7z11_validation.xml.gz | 117 KB | Display | |
Data in CIF | 7z11_validation.cif.gz | 178.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/7z11 ftp://data.pdbj.org/pub/pdb/validation_reports/z1/7z11 | HTTPS FTP |
-Related structure data
Related structure data | 14437MC 7z34C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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 S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: AFG2, DRG1, YLR397C, L8084.16 / Production host: Saccharomyces cerevisiae BY4743 (yeast) References: UniProt: P32794, non-chaperonin molecular chaperone ATPase #2: Protein/peptide | | Mass: 1720.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Production host: Saccharomyces cerevisiae BY4743 (yeast) #3: Chemical | ChemComp-AGS / 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: AFG2 hexamer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Source (recombinant) | Organism: Saccharomyces cerevisiae BY4743 (yeast) |
Buffer solution | pH: 7.6 |
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 | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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 / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
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 slit width: 20 eV |
-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: 3148330 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114728 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficient | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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