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Yorodumi- EMDB-43027: 60S ribosome biogenesis intermediate (Dbp10 post-catalytic struct... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43027 | ||||||||||||
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Title | 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) | ||||||||||||
Map data | 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) | ||||||||||||
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 / Noc1p-Noc2p complex / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / Noc2p-Noc3p complex / rRNA (guanosine-2'-O-)-methyltransferase activity / 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) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity ...25S rRNA (cytosine2870-C5)-methyltransferase / Noc1p-Noc2p complex / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / Noc2p-Noc3p complex / rRNA (guanosine-2'-O-)-methyltransferase activity / 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) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / 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 / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear pre-replicative 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 / 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) / 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) / protein-RNA complex assembly / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / DNA replication initiation / 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) / regulation of translational fidelity / 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 / protein transport / ribosome biogenesis / 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 / translation / cell division / mRNA binding / GTPase activity / chromatin binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / 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) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.66 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_43027.map.gz | 166.7 MB | EMDB map data format | |
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Header (meta data) | emd-43027-v30.xml emd-43027.xml | 85.7 KB 85.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43027_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_43027.png | 92.3 KB | ||
Filedesc metadata | emd-43027.cif.gz | 20 KB | ||
Others | emd_43027_half_map_1.map.gz emd_43027_half_map_2.map.gz | 140.9 MB 140.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43027 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43027 | HTTPS FTP |
-Related structure data
Related structure data | 8v87MC 8v83C 8v84C 8v85C 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_43027.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map) | ||||||||||||||||||||
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: Half Map A
File | emd_43027_half_map_1.map | ||||||||||||
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Annotation | Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B
File | emd_43027_half_map_2.map | ||||||||||||
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Annotation | Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 60S ribosome biogenesis intermediate
+Supramolecule #1: 60S ribosome biogenesis intermediate
+Macromolecule #1: 25S ribosomal RNA
+Macromolecule #2: 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: Nucleolar complex protein 2
+Macromolecule #7: Ribosome biogenesis protein BRX1
+Macromolecule #8: 60S ribosomal protein L3
+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: Nucleolar complex-associated protein 3
+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: 60S ribosomal protein L19-A
+Macromolecule #25: Large ribosomal subunit protein eL20A
+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: Large ribosomal subunit protein uL1A
+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 ribosome subunit biogenesis protein NIP7
+Macromolecule #44: Ribosome biogenesis protein ERB1
+Macromolecule #45: Pescadillo homolog
+Macromolecule #46: Ribosome biogenesis protein 15
+Macromolecule #47: YTM1 isoform 1
+Macromolecule #48: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
+Macromolecule #49: Ribosome biogenesis protein NSA2
+Macromolecule #50: Nuclear GTP-binding protein NUG1
+Macromolecule #51: Ribosome biogenesis protein RLP7
+Macromolecule #52: Ribosome biogenesis protein RLP24
+Macromolecule #53: Nucleolar protein 16
+Macromolecule #54: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+Macromolecule #55: Eukaryotic translation initiation factor 6
+Macromolecule #56: UPF0642 protein YBL028C
+Macromolecule #57: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #58: MAGNESIUM ION
+Macromolecule #59: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #60: POTASSIUM ION
+Macromolecule #61: 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 / Instrument: FEI VITROBOT MARK IV |
-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 |