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Yorodumi- EMDB-26485: Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26485 | |||||||||
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Title | Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922 | |||||||||
Map data | Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922, combined local refinement | |||||||||
Sample |
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Function / homology | Function and homology information protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / 7S RNA binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / Major pathway of rRNA processing in the nucleolus and cytosol ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / 7S RNA binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / ATPase activator activity / 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 / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / protein-RNA complex assembly / ribosomal large subunit export from nucleus / regulation of translational fidelity / 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) / ribosomal subunit export from nucleus / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / ribosomal large subunit biogenesis / maturation of LSU-rRNA / translation initiation factor activity / nuclear periphery / assembly of large subunit precursor of preribosome / small-subunit processome / cytosolic ribosome assembly / maintenance of translational fidelity / macroautophagy / ribosomal large subunit assembly / rRNA processing / protein transport / ribosome biogenesis / large ribosomal subunit rRNA binding / 5S rRNA binding / ATPase binding / cytoplasmic translation / cytosolic large ribosomal subunit / nucleic acid binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / GTPase activity / GTP binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Yelland JN / Bravo JPK / Black JJB / Taylor DW / Johnson AW | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: A single 2'-O-methylation of ribosomal RNA gates assembly of a functional ribosome. Authors: James N Yelland / Jack P K Bravo / Joshua J Black / David W Taylor / Arlen W Johnson / Abstract: RNA modifications are widespread in biology and abundant in ribosomal RNA. However, the importance of these modifications is not well understood. We show that methylation of a single nucleotide, in ...RNA modifications are widespread in biology and abundant in ribosomal RNA. However, the importance of these modifications is not well understood. We show that methylation of a single nucleotide, in the catalytic center of the large subunit, gates ribosome assembly. Massively parallel mutational scanning of the essential nuclear GTPase Nog2 identified important interactions with rRNA, particularly with the 2'-O-methylated A-site base Gm2922. We found that methylation of G2922 is needed for assembly and efficient nuclear export of the large subunit. Critically, we identified single amino acid changes in Nog2 that completely bypass dependence on G2922 methylation and used cryoelectron microscopy to directly visualize how methylation flips Gm2922 into the active site channel of Nog2. This work demonstrates that a single RNA modification is a critical checkpoint in ribosome biogenesis, suggesting that such modifications can play an important role in regulation and assembly of macromolecular machines. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26485.map.gz | 239.1 MB | EMDB map data format | |
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Header (meta data) | emd-26485-v30.xml emd-26485.xml | 73.2 KB 73.2 KB | Display Display | EMDB header |
Images | emd_26485.png | 80.8 KB | ||
Masks | emd_26485_msk_1.map | 512 MB | Mask map | |
Others | emd_26485_additional_1.map.gz emd_26485_half_map_1.map.gz emd_26485_half_map_2.map.gz | 256.4 MB 475.4 MB 475.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26485 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26485 | HTTPS FTP |
-Related structure data
Related structure data | 7ug6MC M: atomic model generated by this map C: citing same article (ref.) |
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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_26485.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922, combined local refinement | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.81 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26485_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922,...
File | emd_26485_additional_1.map | ||||||||||||
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Annotation | Cryo-EM structure of pre-60S ribosomal subunit, unmethylated G2922, pre-local refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 1
File | emd_26485_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_26485_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Nucle(ol)ar intermediate of large ribosomal subunit biogenesis, i...
+Supramolecule #1: Nucle(ol)ar intermediate of large ribosomal subunit biogenesis, i...
+Macromolecule #1: 25S rRNA
+Macromolecule #2: 5.8S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #4: 60S ribosomal protein L30
+Macromolecule #5: 60S ribosomal protein L2-A
+Macromolecule #6: 60S ribosomal protein L3
+Macromolecule #7: 60S ribosomal protein L4-A
+Macromolecule #8: 60S ribosomal protein L5
+Macromolecule #9: 60S ribosomal protein L6-A
+Macromolecule #10: 60S ribosomal protein L7-A
+Macromolecule #11: 60S ribosomal protein L8-A
+Macromolecule #12: 60S ribosomal protein L9-A
+Macromolecule #13: Bud site selection protein 20
+Macromolecule #14: 60S ribosomal protein L11-A
+Macromolecule #15: 60S ribosomal protein L13-A
+Macromolecule #16: 60S ribosomal protein L14-A
+Macromolecule #17: 60S ribosomal protein L15-A
+Macromolecule #18: 60S ribosomal protein L16-A
+Macromolecule #19: 60S ribosomal protein L17-A
+Macromolecule #20: 60S ribosomal protein L18-A
+Macromolecule #21: 60S ribosomal protein L19-A
+Macromolecule #22: 60S ribosomal protein L20-A
+Macromolecule #23: 60S ribosomal protein L21-A
+Macromolecule #24: 60S ribosomal protein L22-A
+Macromolecule #25: 60S ribosomal protein L23-A
+Macromolecule #26: Ribosome assembly factor MRT4
+Macromolecule #27: 60S ribosomal protein L25
+Macromolecule #28: 60S ribosomal protein L26-A
+Macromolecule #29: 60S ribosomal protein L27-A
+Macromolecule #30: 60S ribosomal protein L28
+Macromolecule #31: Nucleolar GTP-binding protein 1
+Macromolecule #32: Ribosome biogenesis protein ALB1
+Macromolecule #33: 60S ribosomal protein L31-A
+Macromolecule #34: 60S ribosomal protein L32
+Macromolecule #35: 60S ribosomal protein L33-A
+Macromolecule #36: 60S ribosomal protein L34-A
+Macromolecule #37: 60S ribosomal protein L35-A
+Macromolecule #38: 60S ribosomal protein L36-A
+Macromolecule #39: 60S ribosomal protein L37-A
+Macromolecule #40: 60S ribosomal protein L38
+Macromolecule #41: 60S ribosomal protein L39
+Macromolecule #42: Nucleolar GTP-binding protein 2
+Macromolecule #43: 60S ribosomal protein L43-A
+Macromolecule #44: 60S ribosomal protein L12-A
+Macromolecule #45: Ribosome biogenesis protein NSA2
+Macromolecule #46: Nuclear GTP-binding protein NUG1
+Macromolecule #47: Ribosome biogenesis protein RLP24
+Macromolecule #48: Ribosome biogenesis protein RPF2
+Macromolecule #49: Regulator of ribosome biosynthesis
+Macromolecule #50: Ribosome assembly protein 4
+Macromolecule #51: Eukaryotic translation initiation factor 6
+Macromolecule #52: UPF0642 protein YBL028C
+Macromolecule #53: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #54: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: One blotting step of 2 seconds at force 0. |
-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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -2.5 µm / Nominal defocus min: -1.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: RANDOM ASSIGNMENT |
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Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15954 |