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- EMDB-11362: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11362 | |||||||||
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Title | Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-B (Poly-Ala) | |||||||||
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![]() | ribosome / 90S pre-ribosome / 40S pre-ribosome / A1 cleavage / Dhr1 | |||||||||
Function / homology | ![]() 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / CURI complex / UTP-C complex / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity ...18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase / 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity / regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / CURI complex / UTP-C complex / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / nuclear microtubule / 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) / septum digestion after cytokinesis / tRNA export from nucleus / 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 primary transcript binding / Negative regulators of DDX58/IFIH1 signaling / rRNA base methylation / sno(s)RNA-containing ribonucleoprotein complex / mTORC1-mediated signalling / Protein hydroxylation / rRNA methylation / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / U3 snoRNA binding / 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 / establishment of cell polarity / snoRNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / nucleolar large rRNA transcription by RNA polymerase I / 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 / regulation of translational fidelity / Ub-specific processing proteases / 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) / enzyme activator activity / RNA endonuclease activity / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / helicase activity / maturation of SSU-rRNA / small-subunit processome / 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 / cell cycle / 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 | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
![]() | Cheng J / Lau B | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 31.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 63.3 KB 63.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.1 KB | Display | ![]() |
Images | ![]() | 110 KB | ||
Filedesc metadata | ![]() | 17.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 419.3 KB | Display | ![]() |
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Full document | ![]() | 418.8 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6zqfMC ![]() 6zqaC ![]() 6zqbC ![]() 6zqcC ![]() 6zqdC ![]() 6zqeC ![]() 6zqgC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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Sample components
+Entire : 90S pre-ribbosome state Dis-B
+Supramolecule #1: 90S pre-ribbosome state Dis-B
+Macromolecule #1: Periodic tryptophan protein 2
+Macromolecule #2: Nucleolar complex protein 14
+Macromolecule #3: Something about silencing protein 10
+Macromolecule #4: U3 small nucleolar RNA-associated protein 12
+Macromolecule #5: U3 small nucleolar RNA-associated protein 13
+Macromolecule #6: Nucleolar complex protein 4
+Macromolecule #7: U3 small nucleolar RNA-associated protein 21
+Macromolecule #8: U3 small nucleolar RNA-associated protein 22
+Macromolecule #9: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #10: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #11: U3 small nucleolar RNA-associated protein MPP10
+Macromolecule #12: Ribosome biogenesis protein BMS1
+Macromolecule #13: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #14: Ribosomal RNA-processing protein 7
+Macromolecule #15: Probable ATP-dependent RNA helicase DHR1
+Macromolecule #16: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #17: Essential nuclear protein 1
+Macromolecule #18: Dimethyladenosine transferase
+Macromolecule #19: Pre-rRNA-processing protein PNO1
+Macromolecule #20: Rps5p
+Macromolecule #21: 40S ribosomal protein S16-A
+Macromolecule #22: 40S ribosomal protein S18-A
+Macromolecule #23: 40S ribosomal protein S19-A
+Macromolecule #24: 40S ribosomal protein S28-A
+Macromolecule #27: 40S ribosomal protein S1-A
+Macromolecule #28: 40S ribosomal protein S4-A
+Macromolecule #29: 40S ribosomal protein S6-A
+Macromolecule #30: 40S ribosomal protein S7-A
+Macromolecule #31: 40S ribosomal protein S8-A
+Macromolecule #32: 40S ribosomal protein S9-A
+Macromolecule #33: 40S ribosomal protein S11-A
+Macromolecule #34: 40S ribosomal protein S13
+Macromolecule #35: 40S ribosomal protein S14-A
+Macromolecule #36: 40S ribosomal protein S25-A
+Macromolecule #37: 40S ribosomal protein S22-A
+Macromolecule #38: 40S ribosomal protein S23-A
+Macromolecule #39: 40S ribosomal protein S24-A
+Macromolecule #40: 40S ribosomal protein S27-A
+Macromolecule #25: 5ETS RNA
+Macromolecule #26: 18S rRNA
+Macromolecule #41: U3 snoRNA
+Macromolecule #42: 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: 7.4 |
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Grid | Model: Quantifoil / Material: COPPER / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |