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Yorodumi- EMDB-11360: 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-11360 | |||||||||
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| Title | Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Post-A1 | |||||||||
Map data | main map | |||||||||
Sample |
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Keywords | ribosome / 90S pre-ribosome / 40S pre-ribosome / A1 cleavage / Dhr1 | |||||||||
| Function / homology | Function and homology information18S 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 / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Noc4p-Nop14p complex ...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 / box H/ACA snoRNA binding / RNA fragment catabolic process / rRNA small subunit pseudouridine methyltransferase Nep1 / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Noc4p-Nop14p complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / Pwp2p-containing subcomplex of 90S preribosome / snoRNA guided rRNA 2'-O-methylation / nuclear microtubule / Mpp10 complex / rRNA (pseudouridine) methyltransferase activity / box C/D sno(s)RNA binding / rRNA modification / histone H2AQ104 methyltransferase activity / septum digestion after cytokinesis / regulation of rRNA processing / rRNA (adenine-N6,N6-)-dimethyltransferase activity / tRNA re-export from nucleus / snRNA binding / RNA folding chaperone / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / rDNA heterochromatin / 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) / regulation of transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D methylation guide snoRNP complex / U4/U6 snRNP / positive regulation of rRNA processing / tRNA export from nucleus / single-stranded telomeric DNA binding / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / Negative regulators of DDX58/IFIH1 signaling / rRNA base methylation / U4 snRNA binding / O-methyltransferase activity / SUMOylation of RNA binding proteins / 90S preribosome assembly / protein localization to nucleolus / mTORC1-mediated signalling / rRNA methylation / Protein hydroxylation / U4 snRNP / poly(U) RNA binding / U3 snoRNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / poly(A)+ mRNA export from nucleus / Translation initiation complex formation / Ribosomal scanning and start codon recognition / snoRNA binding / precatalytic spliceosome / preribosome, small subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / establishment of cell polarity / spliceosomal complex assembly / positive regulation of transcription by RNA polymerase I / SRP-dependent cotranslational protein targeting to membrane / nucleolar large rRNA transcription by RNA polymerase I / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / Ub-specific processing proteases / proteasome assembly / ribosomal subunit export from nucleus / RNA processing / 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) / U4/U6 x U5 tri-snRNP complex / ribosomal small subunit export from nucleus / RNA endonuclease activity / nuclear periphery / Transferases; Transferring one-carbon groups; Methyltransferases / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / spliceosomal complex / small-subunit processome / translational initiation / enzyme activator activity / helicase activity / mRNA splicing, via spliceosome / maintenance of translational fidelity / rRNA processing / peroxisome / unfolded protein binding / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly Similarity search - Function | |||||||||
| Biological species | ![]() ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Cheng J / Lau B | |||||||||
Citation | Journal: Science / Year: 2020Title: 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. | |||||||||
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Structure visualization
| Movie |
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| Structure viewer | EM map: SurfView Molmil Jmol/JSmol |
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_11360.map.gz | 52.9 MB | EMDB map data format | |
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| Header (meta data) | emd-11360-v30.xml emd-11360.xml | 109.6 KB 109.6 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_11360_fsc.xml | 17.1 KB | Display | FSC data file |
| Images | emd_11360.png | 187.6 KB | ||
| Filedesc metadata | emd-11360.cif.gz | 28.2 KB | ||
| Others | emd_11360_additional_1.map.gz emd_11360_additional_2.map.gz emd_11360_additional_3.map.gz emd_11360_additional_4.map.gz | 10 MB 18 MB 9 MB 9.5 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11360 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11360 | HTTPS FTP |
-Validation report
| Summary document | emd_11360_validation.pdf.gz | 489.6 KB | Display | EMDB validaton report |
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| Full document | emd_11360_full_validation.pdf.gz | 489.2 KB | Display | |
| Data in XML | emd_11360_validation.xml.gz | 15.4 KB | Display | |
| Data in CIF | emd_11360_validation.cif.gz | 21.2 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11360 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11360 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 6zqdMC ![]() 6zqaC ![]() 6zqbC ![]() 6zqcC ![]() 6zqeC ![]() 6zqfC ![]() 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 | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_11360.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Annotation | main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.084 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 Head
| File | emd_11360_additional_1.map | ||||||||||||
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| Annotation | multibody refine focus Head | ||||||||||||
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-Additional map: Multibody refine focus Body
| File | emd_11360_additional_2.map | ||||||||||||
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| Annotation | Multibody refine focus Body | ||||||||||||
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-Additional map: Multibody refine focus Platform
| File | emd_11360_additional_3.map | ||||||||||||
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| Annotation | Multibody refine focus Platform | ||||||||||||
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-Additional map: Multibody refine focus Base
| File | emd_11360_additional_4.map | ||||||||||||
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| Annotation | Multibody refine focus Base | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : 90S pre-ribbosome state Post-A1
+Supramolecule #1: 90S pre-ribbosome state Post-A1
+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 20
+Macromolecule #21: U3 small nucleolar RNA-associated protein 21
+Macromolecule #22: U3 small nucleolar RNA-associated protein 22
+Macromolecule #23: rRNA-processing protein FCF1
+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: Probable ATP-dependent RNA helicase DHR1
+Macromolecule #36: Ribosomal RNA small subunit methyltransferase NEP1
+Macromolecule #37: Essential nuclear protein 1
+Macromolecule #38: rRNA biogenesis protein RRP5
+Macromolecule #39: Dimethyladenosine transferase
+Macromolecule #40: rRNA-processing protein FCF2
+Macromolecule #41: Protein SOF1
+Macromolecule #42: 40S ribosomal protein S27-A
+Macromolecule #43: Pre-rRNA-processing protein PNO1
+Macromolecule #44: 40S ribosomal protein S1-A
+Macromolecule #45: 40S ribosomal protein S4-A
+Macromolecule #46: Rps5p
+Macromolecule #47: 40S ribosomal protein S6-A
+Macromolecule #48: 40S ribosomal protein S7-A
+Macromolecule #49: 40S ribosomal protein S8-A
+Macromolecule #50: 40S ribosomal protein S9-A
+Macromolecule #51: 40S ribosomal protein S11-A
+Macromolecule #52: 40S ribosomal protein S13
+Macromolecule #53: 40S ribosomal protein S14-A
+Macromolecule #54: 40S ribosomal protein S16-A
+Macromolecule #55: 40S ribosomal protein S18-A
+Macromolecule #56: 40S ribosomal protein S19-A
+Macromolecule #57: 40S ribosomal protein S22-A
+Macromolecule #58: 40S ribosomal protein S23-A
+Macromolecule #59: 40S ribosomal protein S24-A
+Macromolecule #60: 40S ribosomal protein S28-A
+Macromolecule #61: 5ETS RNA
+Macromolecule #62: 18S rRNA
+Macromolecule #63: U3 snoRNA
+Macromolecule #64: ZINC ION
+Macromolecule #65: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #66: MAGNESIUM ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | 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 | #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: FEI FALCON II (4k x 4k) / #1 - Average electron dose: 28.0 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 |
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