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Yorodumi- EMDB-11357: Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cere... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11357 | |||||||||
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Title | Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state A (Poly-Ala) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ribosome / 90S pre-ribosome / 40S pre-ribosome / A1 cleavage / Dhr1 | |||||||||
Function / homology | Function and homology information regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / nuclear microtubule / t-UTP complex / Mpp10 complex ...regulation of ribosomal protein gene transcription by RNA polymerase II / rRNA small subunit pseudouridine methyltransferase Nep1 / Noc4p-Nop14p complex / RNA fragment catabolic process / rRNA 2'-O-methylation / CURI complex / UTP-C complex / nuclear microtubule / t-UTP complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / rRNA (pseudouridine) methyltransferase activity / rRNA modification / regulation of rRNA processing / histone H2AQ104 methyltransferase activity / snRNA binding / tRNA re-export from nucleus / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / regulation of transcription by RNA polymerase I / box C/D sno(s)RNA 3'-end processing / rDNA heterochromatin / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of rRNA processing / single-stranded telomeric DNA binding / U4/U6 snRNP / tRNA export from nucleus / rRNA base methylation / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding / SUMOylation of RNA binding proteins / O-methyltransferase activity / protein localization to nucleolus / U4 snRNA binding / sno(s)RNA-containing ribonucleoprotein complex / box C/D methylation guide snoRNP complex / Protein hydroxylation / rRNA methylation / U4 snRNP / 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 / establishment of cell polarity / snoRNA binding / precatalytic spliceosome / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / 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 / 90S preribosome / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / RNA processing / 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) / U4/U6 x U5 tri-snRNP complex / enzyme activator activity / RNA endonuclease activity / Transferases; Transferring one-carbon groups; Methyltransferases / nuclear periphery / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / spliceosomal complex / maintenance of translational fidelity / mRNA splicing, via spliceosome / rRNA processing / unfolded protein binding / ribosome biogenesis / peroxisome / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.4 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_11357.map.gz | 44.8 MB | EMDB map data format | |
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Header (meta data) | emd-11357-v30.xml emd-11357.xml | 89.9 KB 89.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11357_fsc.xml | 17.1 KB | Display | FSC data file |
Images | emd_11357.png | 148.7 KB | ||
Filedesc metadata | emd-11357.cif.gz | 24.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11357 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11357 | HTTPS FTP |
-Validation report
Summary document | emd_11357_validation.pdf.gz | 280 KB | Display | EMDB validaton report |
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Full document | emd_11357_full_validation.pdf.gz | 279.1 KB | Display | |
Data in XML | emd_11357_validation.xml.gz | 15.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11357 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11357 | HTTPS FTP |
-Related structure data
Related structure data | 6zqaMC 6zqbC 6zqcC 6zqdC 6zqeC 6zqfC 6zqgC 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_11357.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Sample components
+Entire : 90S pre-ribbosome state A
+Supramolecule #1: 90S pre-ribbosome state A
+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 4
+Macromolecule #5: U3 small nucleolar RNA-associated protein 5
+Macromolecule #6: U3 small nucleolar RNA-associated protein 6
+Macromolecule #7: U3 small nucleolar RNA-associated protein 7
+Macromolecule #8: U3 small nucleolar RNA-associated protein 8
+Macromolecule #9: U3 small nucleolar RNA-associated protein 9
+Macromolecule #10: U3 small nucleolar RNA-associated protein 10
+Macromolecule #11: U3 small nucleolar RNA-associated protein 11
+Macromolecule #12: U3 small nucleolar RNA-associated protein 12
+Macromolecule #13: U3 small nucleolar RNA-associated protein 13
+Macromolecule #14: U3 small nucleolar RNA-associated protein 14
+Macromolecule #15: U3 small nucleolar RNA-associated protein 15
+Macromolecule #16: Bud site selection protein 21
+Macromolecule #17: NET1-associated nuclear protein 1
+Macromolecule #18: U3 small nucleolar RNA-associated protein 18
+Macromolecule #19: Nucleolar complex protein 4
+Macromolecule #20: U3 small nucleolar RNA-associated protein 21
+Macromolecule #21: U3 small nucleolar RNA-associated protein 22
+Macromolecule #22: rRNA-processing protein FCF1
+Macromolecule #23: Ribosome biogenesis protein UTP30
+Macromolecule #24: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #25: Nucleolar protein 56
+Macromolecule #26: Nucleolar protein 58
+Macromolecule #27: 13 kDa ribonucleoprotein-associated protein
+Macromolecule #28: Ribosomal RNA-processing protein 9
+Macromolecule #29: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #30: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #31: U3 small nucleolar RNA-associated protein MPP10
+Macromolecule #32: Ribosome biogenesis protein BMS1
+Macromolecule #33: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #34: Ribosomal RNA-processing protein 7
+Macromolecule #35: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #36: Essential nuclear protein 1
+Macromolecule #37: Pre-rRNA-processing protein PNO1
+Macromolecule #38: rRNA-processing protein FCF2
+Macromolecule #39: Protein FAF1
+Macromolecule #40: KRR1 small subunit processome component
+Macromolecule #41: Protein SOF1
+Macromolecule #42: Regulator of rDNA transcription protein 14
+Macromolecule #43: 40S ribosomal protein S1-A
+Macromolecule #44: Rps5p
+Macromolecule #45: 40S ribosomal protein S7-A
+Macromolecule #46: 40S ribosomal protein S9-A
+Macromolecule #47: 40S ribosomal protein S13
+Macromolecule #48: 40S ribosomal protein S14-A
+Macromolecule #49: 40S ribosomal protein S16-A
+Macromolecule #50: 40S ribosomal protein S18-A
+Macromolecule #51: 40S ribosomal protein S22-A
+Macromolecule #52: 40S ribosomal protein S23-A
+Macromolecule #53: 40S ribosomal protein S27-A
+Macromolecule #54: 40S ribosomal protein S28-A
+Macromolecule #55: 5ETS RNA
+Macromolecule #56: 18S rRNA
+Macromolecule #57: U3 snoRNA
+Macromolecule #58: ZINC ION
+Macromolecule #59: MAGNESIUM ION
+Macromolecule #60: GUANOSINE-5'-TRIPHOSPHATE
-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 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Average electron dose: 44.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - 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 |