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Yorodumi- EMDB-11363: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11363 | |||||||||
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Title | Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-C | |||||||||
Map data | Multibody refine focus 3domain | |||||||||
Sample |
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Keywords | ribosome / 90S pre-ribosome / 40S pre-ribosome / A1 cleavage / Dhr1 | |||||||||
Function / homology | Function and homology information 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / nuclear microtubule / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / rRNA (adenine-N6,N6-)-dimethyltransferase activity ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / nuclear microtubule / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / rRNA (adenine-N6,N6-)-dimethyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / single-stranded telomeric DNA binding / rRNA base methylation / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / U3 snoRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / poly(A)+ mRNA export from nucleus / preribosome, small subunit precursor / snoRNA binding / 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 / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / 90S preribosome / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / ribosomal small 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) / enzyme activator activity / RNA endonuclease activity / nuclear periphery / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / helicase activity / maturation of SSU-rRNA / small-subunit processome / translational initiation / maintenance of translational fidelity / rRNA processing / unfolded protein binding / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / ribosome / RNA helicase / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Cheng J / Lau B | |||||||||
Citation | Journal: Science / Year: 2020 Title: 90 pre-ribosome transformation into the primordial 40 subunit. Authors: Jingdong Cheng / Benjamin Lau / Giuseppe La Venuta / Michael Ameismeier / Otto Berninghausen / Ed Hurt / Roland Beckmann / Abstract: Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this ...Production of small ribosomal subunits initially requires the formation of a 90 precursor followed by an enigmatic process of restructuring into the primordial pre-40 subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90 pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A, thereby separating the 5'-external transcribed spacer (ETS) from 18 ribosomal RNA. Next, the 5'-ETS and 90 assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40 emerges, still retaining some 90 factors including Dhr1, now ready to unwind the final small nucleolar U3-18 RNA hybrid. Our data shed light on the elusive 90 to pre-40 transition and clarify the principles of assembly and remodeling of large ribonucleoproteins. | |||||||||
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_11363.map.gz | 30.9 MB | EMDB map data format | |
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Header (meta data) | emd-11363-v30.xml emd-11363.xml | 57.1 KB 57.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11363_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_11363.png | 78.2 KB | ||
Filedesc metadata | emd-11363.cif.gz | 15 KB | ||
Others | emd_11363_additional.map.gz | 281.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11363 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11363 | HTTPS FTP |
-Validation report
Summary document | emd_11363_validation.pdf.gz | 410.6 KB | Display | EMDB validaton report |
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Full document | emd_11363_full_validation.pdf.gz | 410.2 KB | Display | |
Data in XML | emd_11363_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | emd_11363_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11363 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11363 | HTTPS FTP |
-Related structure data
Related structure data | 6zqgMC 6zqaC 6zqbC 6zqcC 6zqdC 6zqeC 6zqfC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11363.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Multibody refine focus 3domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Multibody refine focus 3domain
File | emd_11363_additional.map | ||||||||||||
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Annotation | Multibody refine focus 3domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 90S pre-ribbosome state Dis-C
+Supramolecule #1: 90S pre-ribbosome state Dis-C
+Macromolecule #1: Nucleolar complex protein 14
+Macromolecule #2: Something about silencing protein 10
+Macromolecule #3: Noc4,Nucleolar complex protein 4,Noc4
+Macromolecule #4: rRNA-processing protein FCF1
+Macromolecule #5: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #6: U3 small nucleolar RNA-associated protein MPP10
+Macromolecule #7: Ribosome biogenesis protein BMS1
+Macromolecule #8: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #9: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #10: Essential nuclear protein 1
+Macromolecule #11: Dimethyladenosine transferase
+Macromolecule #12: Pre-rRNA-processing protein PNO1
+Macromolecule #13: Rps5p
+Macromolecule #14: 40S ribosomal protein S16-A
+Macromolecule #15: 40S ribosomal protein S18-A,40S ribosomal protein S18-A,Rps18
+Macromolecule #16: 40S ribosomal protein S19-A
+Macromolecule #17: 40S ribosomal protein S28-A
+Macromolecule #19: 40S ribosomal protein S1-A
+Macromolecule #20: 40S ribosomal protein S4-A
+Macromolecule #21: 40S ribosomal protein S6-A
+Macromolecule #22: 40S ribosomal protein S7-A
+Macromolecule #23: 40S ribosomal protein S8-A
+Macromolecule #24: 40S ribosomal protein S9-A
+Macromolecule #25: 40S ribosomal protein S11-A
+Macromolecule #26: 40S ribosomal protein S13
+Macromolecule #27: 40S ribosomal protein S14-A
+Macromolecule #28: 40S ribosomal protein S25-A
+Macromolecule #29: 40S ribosomal protein S22-A
+Macromolecule #30: 40S ribosomal protein S23-A
+Macromolecule #31: 40S ribosomal protein S24-A
+Macromolecule #32: 40S ribosomal protein S27-A
+Macromolecule #33: U3 small nucleolar RNA-associated protein 14
+Macromolecule #34: Probable ATP-dependent RNA helicase DHR1
+Macromolecule #18: 18S rRNA
+Macromolecule #35: U3 snoRNA
+Macromolecule #36: Poly-U RNA
+Macromolecule #37: ZINC ION
+Macromolecule #38: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #39: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil / Material: COPPER / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |