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Yorodumi- EMDB-43021: 60S ribosome biogenesis intermediate (Dbp10 catalytic structure -... -
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-Basic information
Entry | Database: EMDB / ID: EMD-43021 | ||||||||||||
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Title | 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map) | ||||||||||||
Map data | Overall map Dbp10 catalytic intermediate | ||||||||||||
Sample |
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Keywords | Ribosome biogenesis / intermediate DEAD-box ATPase / Ribosome-RNA complex | ||||||||||||
Function / homology | Function and homology information 25S rRNA (cytosine2870-C5)-methyltransferase / snoRNA release from pre-rRNA / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (cytosine-C5-)-methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / intracellular mRNA localization / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex ...25S rRNA (cytosine2870-C5)-methyltransferase / snoRNA release from pre-rRNA / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (cytosine-C5-)-methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / intracellular mRNA localization / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA base methylation / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / positive regulation of ATP-dependent activity / protein folding chaperone complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / nuclear-transcribed mRNA catabolic process / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / regulation of cell size / maturation of 5.8S rRNA / proteasome binding / ribosomal subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / ATPase activator activity / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA transport / ribonucleoprotein complex binding / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translation initiation factor activity / proteasome complex / small-subunit processome / assembly of large subunit precursor of preribosome / nuclear periphery / cytosolic ribosome assembly / maintenance of translational fidelity / macroautophagy / protein catabolic process / ribosomal small subunit biogenesis / ribosomal large subunit assembly / rRNA processing / large ribosomal subunit rRNA binding / protein-macromolecule adaptor activity / nuclear envelope / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / ATPase binding / negative regulation of translation / RNA helicase activity / rRNA binding / ribosome / RNA helicase / structural constituent of ribosome / cell cycle / translation / mRNA binding / GTPase activity / GTP binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae BY4741 (yeast) / Saccharomyces cerevisiae BY4741-AV16 (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||
Authors | Cruz VE / Weirich CS / Peddada N / Erzberger JP | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Commun / Year: 2024 Title: The DEAD-box ATPase Dbp10/DDX54 initiates peptidyl transferase center formation during 60S ribosome biogenesis. Authors: Victor E Cruz / Christine S Weirich / Nagesh Peddada / Jan P Erzberger / Abstract: DEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this ...DEAD-box ATPases play crucial roles in guiding rRNA restructuring events during the biogenesis of large (60S) ribosomal subunits, but their precise molecular functions are currently unknown. In this study, we present cryo-EM reconstructions of nucleolar pre-60S intermediates that reveal an unexpected, alternate secondary structure within the nascent peptidyl-transferase-center (PTC). Our analysis of three sequential nucleolar pre-60S intermediates reveals that the DEAD-box ATPase Dbp10/DDX54 remodels this alternate base pairing and enables the formation of the rRNA junction that anchors the mature form of the universally conserved PTC A-loop. Post-catalysis, Dbp10 captures rRNA helix H61, initiating the concerted exchange of biogenesis factors during late nucleolar 60S maturation. Our findings show that Dbp10 activity is essential for the formation of the ribosome active site and reveal how this function is integrated with subsequent assembly steps to drive the biogenesis of the large ribosomal subunit. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43021.map.gz | 229.1 MB | EMDB map data format | |
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Header (meta data) | emd-43021-v30.xml emd-43021.xml | 76.5 KB 76.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43021_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_43021.png | 105.7 KB | ||
Filedesc metadata | emd-43021.cif.gz | 18.5 KB | ||
Others | emd_43021_half_map_1.map.gz emd_43021_half_map_2.map.gz | 194.9 MB 194.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43021 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43021 | HTTPS FTP |
-Related structure data
Related structure data | 8v84MC 8v83C 8v85C 8v87C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_43021.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Overall map Dbp10 catalytic intermediate | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Overall half-map 1 Dbp10 catalytic intermediate
File | emd_43021_half_map_1.map | ||||||||||||
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Annotation | Overall half-map 1 Dbp10 catalytic intermediate | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Overall half-map 2 Dbp10 catalytic intermediate
File | emd_43021_half_map_2.map | ||||||||||||
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Annotation | Overall half-map 2 Dbp10 catalytic intermediate | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 60S ribosome biogenesis intermediate
+Supramolecule #1: 60S ribosome biogenesis intermediate
+Macromolecule #1: Saccharomyces cerevisiae 25S ribosomal RNA
+Macromolecule #2: Saccharomyces cerevisiae 5.8S ribosomal RNA
+Macromolecule #4: ITS2 RNA
+Macromolecule #3: ATP-dependent RNA helicase DBP10
+Macromolecule #5: 60S ribosomal subunit assembly/export protein LOC1
+Macromolecule #6: Ribosomal RNA-processing protein 14
+Macromolecule #7: Ribosome biogenesis protein BRX1
+Macromolecule #8: Large ribosomal subunit protein uL3
+Macromolecule #9: 60S ribosomal protein L4-A
+Macromolecule #10: ATP-dependent RNA helicase HAS1
+Macromolecule #11: 60S ribosomal protein L6-A
+Macromolecule #12: 60S ribosomal protein L7-A
+Macromolecule #13: Large ribosomal subunit protein eL8A
+Macromolecule #14: Large ribosomal subunit protein uL6A
+Macromolecule #15: Ribosome biogenesis protein NSA1
+Macromolecule #16: rRNA-processing protein EBP2
+Macromolecule #17: Proteasome-interacting protein CIC1
+Macromolecule #18: 60S ribosomal protein L13-A
+Macromolecule #19: 60S ribosomal protein L14-A
+Macromolecule #20: Large ribosomal subunit protein eL15A
+Macromolecule #21: Large ribosomal subunit protein uL13A
+Macromolecule #22: 60S ribosomal protein L17-A
+Macromolecule #23: 60S ribosomal protein L18-A
+Macromolecule #24: Protein MAK16
+Macromolecule #25: Large ribosomal subunit protein eL20A
+Macromolecule #26: Ribosomal RNA-processing protein 15
+Macromolecule #27: 60S ribosomal protein L23-A
+Macromolecule #28: Ribosome assembly factor MRT4
+Macromolecule #29: 60S ribosomal protein L26-A
+Macromolecule #30: Ribosome biogenesis protein SSF1
+Macromolecule #31: Large ribosomal subunit protein uL1A
+Macromolecule #32: Nucleolar GTP-binding protein 1
+Macromolecule #33: 60S ribosomal protein L32
+Macromolecule #34: 60S ribosomal protein L33-A
+Macromolecule #35: 60S ribosomal protein L35-A
+Macromolecule #36: 60S ribosomal protein L36-A
+Macromolecule #37: 60S ribosomal protein L37-A
+Macromolecule #38: 60S ribosome subunit biogenesis protein NIP7
+Macromolecule #39: Ribosome biogenesis protein ERB1
+Macromolecule #40: Pescadillo homolog
+Macromolecule #41: Ribosome biogenesis protein 15
+Macromolecule #42: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
+Macromolecule #43: Ribosome biogenesis protein NSA2
+Macromolecule #44: Ribosome biogenesis protein RLP7
+Macromolecule #45: Ribosome biogenesis protein RLP24
+Macromolecule #46: Nucleolar protein 16
+Macromolecule #47: Ribosomal RNA-processing protein 1
+Macromolecule #48: Ribosome production factor 1
+Macromolecule #49: Eukaryotic translation initiation factor 6
+Macromolecule #50: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #51: MAGNESIUM ION
+Macromolecule #52: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.3 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |