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- EMDB-12910: Nog1-TAP associated immature ribosomal particles from S. cerevisi... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12910 | |||||||||
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Title | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C | |||||||||
![]() | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C, full map | |||||||||
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Function / homology | ![]() 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / snoRNA release from pre-rRNA / protein-RNA complex remodeling / 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 (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / PeBoW complex ...27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / snoRNA release from pre-rRNA / protein-RNA complex remodeling / 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 (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / positive regulation of ATP-dependent activity / 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) / 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) / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / chromosome organization / protein-RNA complex assembly / regulation of translational fidelity / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / translation initiation factor activity / proteasome complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / ribosomal large subunit biogenesis / cytosolic ribosome assembly / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / protein catabolic process / ribosomal large subunit assembly / rRNA processing / protein-macromolecule adaptor activity / nuclear envelope / ribosomal small subunit biogenesis / ATPase binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / negative regulation of translation / ribosome / RNA helicase / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Milkereit P / Poell G | |||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 193.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 68.5 KB 68.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.3 KB | Display | ![]() |
Images | ![]() | 126.5 KB | ||
Others | ![]() ![]() | 193.6 MB 193.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 563.7 KB | Display | ![]() |
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Full document | ![]() | 563.3 KB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ohvMC ![]() 7of1C ![]() 7oh3C ![]() 7ohpC ![]() 7ohqC ![]() 7ohrC ![]() 7ohsC ![]() 7ohtC ![]() 7ohuC ![]() 7ohwC ![]() 7ohxC ![]() 7ohyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 4.9 TB Data #1: Unaligned multiframe micrographs of Nog1-TAP associated immature ribosomal particles from S. cerevisisae depleted of rpL2 [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C, full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 particles from S. cerevisiae...
File | emd_12910_half_map_1.map | ||||||||||||
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Annotation | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C, half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Nog1-TAP associated immature ribosomal particles from S. cerevisiae...
File | emd_12910_half_map_2.map | ||||||||||||
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Annotation | Nog1-TAP associated immature ribosomal particles from S. cerevisiae after rpL2 expression shut down, population C, half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Nog1-TAP associated immature ribosomal particles from cells deple...
+Supramolecule #1: Nog1-TAP associated immature ribosomal particles from cells deple...
+Macromolecule #1: 25S rRNA
+Macromolecule #2: 5.8S rRNA
+Macromolecule #3: ITS2
+Macromolecule #4: Ribosome biogenesis protein BRX1
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4-A
+Macromolecule #7: ATP-dependent RNA helicase HAS1
+Macromolecule #8: 60S ribosomal protein L6-A
+Macromolecule #9: 60S ribosomal protein L7-A
+Macromolecule #10: 60S ribosomal protein L8-A
+Macromolecule #11: 60S ribosomal protein L9-A
+Macromolecule #12: rRNA-processing protein EBP2
+Macromolecule #13: Proteasome-interacting protein CIC1
+Macromolecule #14: 60S ribosomal protein L13-A
+Macromolecule #15: 60S ribosomal protein L14-A
+Macromolecule #16: 60S ribosomal protein L15-A
+Macromolecule #17: 60S ribosomal protein L16-A
+Macromolecule #18: 60S ribosomal protein L17-A
+Macromolecule #19: 60S ribosomal protein L18-A
+Macromolecule #20: 60S ribosomal protein L19-A
+Macromolecule #21: 60S ribosomal protein L20-A
+Macromolecule #22: 60S ribosomal protein L22-A
+Macromolecule #23: 60S ribosomal protein L23-A
+Macromolecule #24: Ribosome assembly factor MRT4
+Macromolecule #25: 60S ribosomal protein L25
+Macromolecule #26: 60S ribosomal protein L26-A
+Macromolecule #27: 60S ribosomal protein L27-A
+Macromolecule #28: 60S ribosomal protein L28
+Macromolecule #29: Nucleolar GTP-binding protein 1
+Macromolecule #30: 60S ribosomal protein L31-A
+Macromolecule #31: 60S ribosomal protein L32
+Macromolecule #32: 60S ribosomal protein L33-A
+Macromolecule #33: 60S ribosomal protein L35-A
+Macromolecule #34: 60S ribosomal protein L36-A
+Macromolecule #35: 60S ribosomal protein L37-A
+Macromolecule #36: 60S ribosomal protein L38
+Macromolecule #37: Ribosome biogenesis protein ERB1
+Macromolecule #38: Pescadillo homolog
+Macromolecule #39: Ribosome biogenesis protein 15
+Macromolecule #40: Ribosome biogenesis protein YTM1
+Macromolecule #41: Ribosome biogenesis protein NSA2
+Macromolecule #42: Ribosome biogenesis protein RLP7
+Macromolecule #43: Ribosome biogenesis protein RLP24
+Macromolecule #44: Nucleolar protein 16
+Macromolecule #45: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+Macromolecule #46: Eukaryotic translation initiation factor 6
+Macromolecule #47: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 - Atmosphere: AIR / Pretreatment - Pressure: 0.4 kPa | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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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: 86.45 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
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 |