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Yorodumi- EMDB-12905: Nog1-TAP associated immature ribosomal particle population C from... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12905 | |||||||||
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Title | Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae | |||||||||
Map data | Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae, full map | |||||||||
Sample |
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Keywords | ribosomal assembly state / RIBOSOME | |||||||||
Function / homology | Function and homology information protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / PeBoW complex / 7S RNA binding / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear exosome (RNase complex) / PeBoW complex / 7S RNA binding / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-mRNA 5'-splice site binding / 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) / proteasome binding / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / ribosomal 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) / translation initiation factor activity / proteasome complex / nuclear periphery / 90S preribosome / 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) / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / small-subunit processome / maintenance of translational fidelity / protein catabolic process / ribosomal large subunit assembly / rRNA processing / protein transport / ribosome biogenesis / protein-macromolecule adaptor activity / ATPase binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Milkereit P / Poell G | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: PLoS One / Year: 2021 Title: Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors. Authors: Gisela Pöll / Michael Pilsl / Joachim Griesenbeck / Herbert Tschochner / Philipp Milkereit / Abstract: In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with ...In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with the stabilisation and maturation of subunit precursors potentially promotes the production of ribosomes with defined composition. To further decipher mechanisms of such an intrinsic quality control pathway we analysed here the contribution of three yeast large ribosomal subunit r-proteins rpL2 (uL2), rpL25 (uL23) and rpL34 (eL34) for intermediate nuclear subunit folding steps. Structure models obtained from single particle cryo-electron microscopy analyses provided evidence for specific and hierarchic effects on the stable positioning and remodelling of large ribosomal subunit domains. Based on these structural and previous biochemical data we discuss possible mechanisms of r-protein dependent hierarchic domain arrangement and the resulting impact on the stability of misassembled subunits. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12905.map.gz | 193.6 MB | EMDB map data format | |
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Header (meta data) | emd-12905-v30.xml emd-12905.xml | 83.4 KB 83.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12905_fsc.xml | 14.2 KB | Display | FSC data file |
Images | emd_12905.png | 122.9 KB | ||
Filedesc metadata | emd-12905.cif.gz | 17.2 KB | ||
Others | emd_12905_half_map_1.map.gz emd_12905_half_map_2.map.gz | 194.2 MB 194.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12905 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12905 | HTTPS FTP |
-Validation report
Summary document | emd_12905_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_12905_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_12905_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | emd_12905_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12905 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12905 | HTTPS FTP |
-Related structure data
Related structure data | 7ohqMC 7of1C 7oh3C 7ohpC 7ohrC 7ohsC 7ohtC 7ohuC 7ohvC 7ohwC 7ohxC 7ohyC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10776 (Title: Nog1 TAP associated immature ribosomal particles from S. cerevisiae Data size: 8.3 TB Data #1: Unaligned multiframe micrographs of Nog1-TAP associated immature ribosomal particles from S. cerevisisae [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12905.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae, full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0635 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Nog1-TAP associated immature ribosomal particle population C from...
File | emd_12905_half_map_1.map | ||||||||||||
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Annotation | Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Nog1-TAP associated immature ribosomal particle population C from...
File | emd_12905_half_map_2.map | ||||||||||||
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Annotation | Nog1-TAP associated immature ribosomal particle population C from S. cerevisiae, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Nog1-TAP associated immature ribosomal particles.
+Supramolecule #1: Nog1-TAP associated immature ribosomal particles.
+Macromolecule #1: 25S rRNA
+Macromolecule #2: 5.8S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #5: ITS2
+Macromolecule #4: rRNA-processing protein CGR1
+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: 60S ribosomal protein L11-A
+Macromolecule #15: Proteasome-interacting protein CIC1
+Macromolecule #16: 60S ribosomal protein L13-A
+Macromolecule #17: 60S ribosomal protein L14-A
+Macromolecule #18: 60S ribosomal protein L15-A
+Macromolecule #19: 60S ribosomal protein L16-A
+Macromolecule #20: 60S ribosomal protein L17-A
+Macromolecule #21: 60S ribosomal protein L18-A
+Macromolecule #22: 60S ribosomal protein L19-A
+Macromolecule #23: 60S ribosomal protein L20-A
+Macromolecule #24: 60S ribosomal protein L21-A
+Macromolecule #25: 60S ribosomal protein L22-A
+Macromolecule #26: 60S ribosomal protein L23-A
+Macromolecule #27: Ribosome assembly factor MRT4
+Macromolecule #28: 60S ribosomal protein L25
+Macromolecule #29: 60S ribosomal protein L26-A
+Macromolecule #30: 60S ribosomal protein L27-A
+Macromolecule #31: 60S ribosomal protein L28
+Macromolecule #32: Nucleolar GTP-binding protein 1
+Macromolecule #33: 60S ribosomal protein L30
+Macromolecule #34: 60S ribosomal protein L31-A
+Macromolecule #35: 60S ribosomal protein L32
+Macromolecule #36: 60S ribosomal protein L33-A
+Macromolecule #37: 60S ribosomal protein L34-A
+Macromolecule #38: 60S ribosomal protein L35-A
+Macromolecule #39: 60S ribosomal protein L36-A
+Macromolecule #40: 60S ribosomal protein L37-A
+Macromolecule #41: 60S ribosomal protein L38
+Macromolecule #42: 60S ribosomal protein L39
+Macromolecule #43: Nucleolar GTP-binding protein 2
+Macromolecule #44: Pescadillo homolog
+Macromolecule #45: Ribosome biogenesis protein 15
+Macromolecule #46: 60S ribosomal protein L43-A
+Macromolecule #47: Ribosome biogenesis protein NOP53
+Macromolecule #48: Ribosome biogenesis protein NSA2
+Macromolecule #49: Nuclear GTP-binding protein NUG1
+Macromolecule #50: Ribosome biogenesis protein RLP7
+Macromolecule #51: Ribosome biogenesis protein RLP24
+Macromolecule #52: Ribosome biogenesis protein RPF2
+Macromolecule #53: Regulator of ribosome biosynthesis
+Macromolecule #54: Ribosome assembly protein 4
+Macromolecule #55: Eukaryotic translation initiation factor 6
+Macromolecule #56: UPF0642 protein YBL028C
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 200 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.4 kPa | ||||||||
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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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 5.16 sec. / Average electron dose: 84.67 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |