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Yorodumi- EMDB-30585: Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1) -
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Open data
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Basic information
| Entry | Database: EMDB / ID: EMD-30585 | |||||||||
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| Title | Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1) | |||||||||
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Keywords | ribosome assembly / 90S to pre-40S transition / cryo-EM / Dhr1 / Utp24 / RIBOSOME | |||||||||
| Function / homology | Function and homology informationregulation of ribosomal protein gene transcription by RNA polymerase II / box H/ACA snoRNA binding / RNA fragment catabolic process / Noc4p-Nop14p complex / rRNA 2'-O-methylation / CURI complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / snoRNA guided rRNA 2'-O-methylation ...regulation of ribosomal protein gene transcription by RNA polymerase II / box H/ACA snoRNA binding / RNA fragment catabolic process / Noc4p-Nop14p complex / rRNA 2'-O-methylation / CURI complex / UTP-C complex / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / t-UTP complex / snoRNA guided rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / Mpp10 complex / rRNA modification / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA binding / regulation of rRNA processing / septum digestion after cytokinesis / snRNA binding / RNA folding chaperone / box C/D sno(s)RNA 3'-end processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / rDNA heterochromatin / 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 / U4 snRNA binding / O-methyltransferase activity / SUMOylation of RNA binding proteins / protein localization to nucleolus / 90S preribosome assembly / 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 / Translation initiation complex formation / Ribosomal scanning and start codon recognition / snoRNA binding / preribosome, small subunit precursor / precatalytic spliceosome / 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 / GTP hydrolysis and joining of the 60S ribosomal subunit / nucleolar large rRNA transcription by RNA polymerase I / 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 / 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 / RNA endonuclease activity / Transferases; Transferring one-carbon groups; Methyltransferases / 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 / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic translation / RNA helicase activity / rRNA binding / structural constituent of ribosome / RNA helicase / ribosome / translation / GTPase activity / mRNA binding / GTP binding / nucleolus Similarity search - Function | |||||||||
| Biological species | ![]() ![]() | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 6.0 Å | |||||||||
Authors | Du Y / Zhang J | |||||||||
| Funding support | China, 2 items
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Citation | Journal: To Be PublishedTitle: Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1) Authors: Ye K | |||||||||
| History |
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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_30585.map.gz | 15.7 MB | EMDB map data format | |
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| Header (meta data) | emd-30585-v30.xml emd-30585.xml | 92.1 KB 92.1 KB | Display Display | EMDB header |
| Images | emd_30585.png | 59.6 KB | ||
| Filedesc metadata | emd-30585.cif.gz | 25.8 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30585 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30585 | HTTPS FTP |
-Validation report
| Summary document | emd_30585_validation.pdf.gz | 400.9 KB | Display | EMDB validaton report |
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| Full document | emd_30585_full_validation.pdf.gz | 400.5 KB | Display | |
| Data in XML | emd_30585_validation.xml.gz | 7.1 KB | Display | |
| Data in CIF | emd_30585_validation.cif.gz | 8.1 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30585 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30585 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7d5tMC ![]() 7d4iC ![]() 7d5sC ![]() 7d63C 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_30585.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.328 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-ribosome (state F1)
+Supramolecule #1: 90S pre-ribosome (state F1)
+Macromolecule #1: U3 snoRNA
+Macromolecule #2: 5' ETS
+Macromolecule #3: 18S rRNA
+Macromolecule #4: 40S ribosomal protein S1-A
+Macromolecule #5: 40S ribosomal protein S4-A
+Macromolecule #6: 40S ribosomal protein S5
+Macromolecule #7: 40S ribosomal protein S6-A
+Macromolecule #8: 40S ribosomal protein S7-A
+Macromolecule #9: 40S ribosomal protein S8-A
+Macromolecule #10: 40S ribosomal protein S9-A
+Macromolecule #11: 40S ribosomal protein S11-A
+Macromolecule #12: 40S ribosomal protein S13
+Macromolecule #13: 40S ribosomal protein S14-A
+Macromolecule #14: 40S ribosomal protein S16-A
+Macromolecule #15: 40S ribosomal protein S22-B
+Macromolecule #16: 40S ribosomal protein S23-A
+Macromolecule #17: 40S ribosomal protein S24-A
+Macromolecule #18: 40S ribosomal protein S27-A
+Macromolecule #19: 40S ribosomal protein S28-A
+Macromolecule #20: rRNA 2'-O-methyltransferase fibrillarin
+Macromolecule #21: Nucleolar protein 56
+Macromolecule #22: Nucleolar protein 58
+Macromolecule #23: Ribosomal RNA-processing protein 9
+Macromolecule #24: 13 kDa ribonucleoprotein-associated protein
+Macromolecule #25: U3 small nucleolar RNA-associated protein 5
+Macromolecule #26: U3 small nucleolar RNA-associated protein 10
+Macromolecule #27: NET1-associated nuclear protein 1
+Macromolecule #28: Periodic tryptophan protein 2
+Macromolecule #29: U3 small nucleolar RNA-associated protein 12
+Macromolecule #30: U3 small nucleolar RNA-associated protein 13
+Macromolecule #31: U3 small nucleolar RNA-associated protein 18
+Macromolecule #32: U3 small nucleolar RNA-associated protein 21
+Macromolecule #33: U3 small nucleolar RNA-associated protein 6
+Macromolecule #34: U3 small nucleolar RNA-associated protein 7
+Macromolecule #35: U3 small nucleolar RNA-associated protein 11
+Macromolecule #36: U3 small nucleolar RNA-associated protein MPP10
+Macromolecule #37: U3 small nucleolar ribonucleoprotein protein IMP3
+Macromolecule #38: U3 small nucleolar ribonucleoprotein protein IMP4
+Macromolecule #39: Something about silencing protein 10
+Macromolecule #40: Protein SOF1
+Macromolecule #41: rRNA-processing protein FCF2
+Macromolecule #42: rRNA-processing protein FCF1
+Macromolecule #43: rRNA biogenesis protein RRP5
+Macromolecule #44: U3 small nucleolar RNA-associated protein 22
+Macromolecule #45: Ribosomal RNA-processing protein 7
+Macromolecule #46: Ribosome biogenesis protein BMS1
+Macromolecule #47: RNA 3'-terminal phosphate cyclase-like protein
+Macromolecule #48: Nucleolar complex protein 14
+Macromolecule #49: U3 small nucleolar RNA-associated protein 20
+Macromolecule #50: U3 small nucleolar RNA-associated protein 14
+Macromolecule #51: Pno1
+Macromolecule #52: Probable ATP-dependent RNA helicase DHR1
+Macromolecule #53: Unassigned peptides 1
+Macromolecule #54: ZINC ION
+Macromolecule #55: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #56: MAGNESIUM ION
+Macromolecule #57: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 2.0 mg/mL | |||||||||
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| Buffer | pH: 7.4 Component:
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| Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 50 sec. | |||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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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) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number grids imaged: 10 / Number real images: 18538 / Average electron dose: 50.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi


Keywords
Authors
China, 2 items
Citation
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