+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14471 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of pre-60S particle bound to DRG1(AFG2) | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | Ribosome biogenesis / AAA-ATPases / large ribosomal subunit / substrate recognition / substrate translocation mechanism / single particle cryo-EM / RIBOSOME | |||||||||
Function / homology | Function and homology information Hydrolases / positive regulation of ATP-dependent activity / protein hexamerization / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / maturation of 5.8S rRNA / non-chaperonin molecular chaperone ATPase / SRP-dependent cotranslational protein targeting to membrane ...Hydrolases / positive regulation of ATP-dependent activity / protein hexamerization / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / maturation of 5.8S rRNA / non-chaperonin molecular chaperone ATPase / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / nuclear-transcribed mRNA catabolic process / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / ribosomal subunit export from nucleus / Neutrophil degranulation / translation initiation factor activity / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / rRNA processing / metallopeptidase activity / protein transport / ribosome biogenesis / ATPase binding / protein-macromolecule adaptor activity / 5S rRNA binding / large ribosomal subunit rRNA binding / nucleic acid binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to xenobiotic stimulus / response to antibiotic / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) / Saccharomyces cerevisiae S288C ATCC 204508 / S288c (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Prattes M / Grishkovskaya I / Bergler H / Haselbach D | |||||||||
Funding support | Austria, 1 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_14471.map.gz | 387.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-14471-v30.xml emd-14471.xml | 77.2 KB 77.2 KB | Display Display | EMDB header |
Images | emd_14471.png | 49 KB | ||
Others | emd_14471_half_map_1.map.gz emd_14471_half_map_2.map.gz | 390.9 MB 390.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14471 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14471 | HTTPS FTP |
-Validation report
Summary document | emd_14471_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_14471_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_14471_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | emd_14471_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14471 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14471 | HTTPS FTP |
-Related structure data
Related structure data | 7z34MC 7z11C C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_14471.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.3375 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_14471_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_14471_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : pre-60S ribosomal particle in complex with DRG1(AFG2)
+Supramolecule #1: pre-60S ribosomal particle in complex with DRG1(AFG2)
+Macromolecule #1: ATPase family gene 2 protein
+Macromolecule #5: Probable metalloprotease ARX1
+Macromolecule #6: 60S ribosomal protein L2-A
+Macromolecule #7: 60S ribosomal protein L3
+Macromolecule #8: 60S ribosomal protein L4-A
+Macromolecule #9: 60S ribosomal protein L5
+Macromolecule #10: 60S ribosomal protein L6-A
+Macromolecule #11: 60S ribosomal protein L7-A
+Macromolecule #12: 60S ribosomal protein L8-A
+Macromolecule #13: 60S ribosomal protein L9-A
+Macromolecule #14: Bud site selection protein 20
+Macromolecule #15: 60S ribosomal protein L11-A
+Macromolecule #16: 60S ribosomal protein L28
+Macromolecule #17: 60S ribosomal protein L13-A
+Macromolecule #18: 60S ribosomal protein L14-A
+Macromolecule #19: 60S ribosomal protein L15-A
+Macromolecule #20: 60S ribosomal protein L16-A
+Macromolecule #21: 60S ribosomal protein L17-A
+Macromolecule #22: 60S ribosomal protein L18-A
+Macromolecule #23: 60S ribosomal protein L19-A
+Macromolecule #24: 60S ribosomal protein L20-A
+Macromolecule #25: 60S ribosomal protein L21-A
+Macromolecule #26: 60S ribosomal protein L22-A
+Macromolecule #27: 60S ribosomal protein L23-A
+Macromolecule #28: Ribosome assembly factor MRT4
+Macromolecule #29: 60S ribosomal protein L25
+Macromolecule #30: 60S ribosomal protein L26-A
+Macromolecule #31: 60S ribosomal protein L27-A
+Macromolecule #32: 60S ribosomal protein L12-A
+Macromolecule #33: Nucleolar GTP-binding protein 1
+Macromolecule #34: 60S ribosomal protein L30
+Macromolecule #35: 60S ribosomal protein L31-A
+Macromolecule #36: 60S ribosomal protein L32
+Macromolecule #37: 60S ribosomal protein L33-A
+Macromolecule #38: 60S ribosomal protein L34-A
+Macromolecule #39: 60S ribosomal protein L35-A
+Macromolecule #40: 60S ribosomal protein L36-A
+Macromolecule #41: 60S ribosomal protein L37-A
+Macromolecule #42: 60S ribosomal protein L38
+Macromolecule #43: 60S ribosomal protein L39
+Macromolecule #44: 60S ribosomal protein L29
+Macromolecule #45: 60S ribosomal protein L43-A
+Macromolecule #46: 60S ribosomal protein L42-A
+Macromolecule #47: Ribosome biogenesis protein NSA2
+Macromolecule #48: Ribosome biogenesis protein RLP24
+Macromolecule #49: 60S ribosomal export protein NMD3
+Macromolecule #50: Eukaryotic translation initiation factor 6
+Macromolecule #51: UPF0642 protein YBL028C
+Macromolecule #52: Unknown peptide
+Macromolecule #53: Unknown protein
+Macromolecule #2: 35S pre-ribosomal RNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: 5.8S rRNA
+Macromolecule #54: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
+Macromolecule #55: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Grid | Model: Quantifoil R1.2/1.3 / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |