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Yorodumi- EMDB-0441: Conformational switches control early maturation of the eukaryoti... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0441 | |||||||||
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Title | Conformational switches control early maturation of the eukaryotic small ribosomal subunit | |||||||||
Map data | masked, sharpened map | |||||||||
Sample |
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Keywords | Ribosome assembly / RIBOSOME | |||||||||
Function / homology | Function and homology information t-UTP complex / RNA fragment catabolic process / rRNA 2'-O-methylation / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / snoRNA guided rRNA 2'-O-methylation / histone H2AQ104 methyltransferase activity / rRNA modification / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA re-export from nucleus ...t-UTP complex / RNA fragment catabolic process / rRNA 2'-O-methylation / Mpp10 complex / Pwp2p-containing subcomplex of 90S preribosome / snoRNA guided rRNA 2'-O-methylation / histone H2AQ104 methyltransferase activity / rRNA modification / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA re-export from nucleus / snRNA binding / box C/D sno(s)RNA 3'-end processing / septum digestion after cytokinesis / regulation of transcription by RNA polymerase I / rRNA methyltransferase activity / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rDNA heterochromatin / positive regulation of rRNA processing / tRNA export from nucleus / box C/D methylation guide snoRNP complex / U4/U6 snRNP / SUMOylation of RNA binding proteins / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / protein localization to nucleolus / O-methyltransferase activity / rRNA methylation / U3 snoRNA binding / U4 snRNP / preribosome, small subunit precursor / snoRNA binding / precatalytic spliceosome / establishment of cell polarity / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / spliceosomal complex assembly / 90S preribosome / 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 / small-subunit processome / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / ribosomal small subunit biogenesis / peroxisome / ribosomal small subunit assembly / tRNA binding / rRNA binding / mRNA binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae BY4741 (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Hunziker M / Barandun J | |||||||||
Funding support | United States, Switzerland, 2 items
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Citation | Journal: Elife / Year: 2019 Title: Conformational switches control early maturation of the eukaryotic small ribosomal subunit. Authors: Mirjam Hunziker / Jonas Barandun / Olga Buzovetsky / Caitlin Steckler / Henrik Molina / Sebastian Klinge / Abstract: Eukaryotic ribosome biogenesis is initiated with the transcription of pre-ribosomal RNA at the 5' external transcribed spacer, which directs the early association of assembly factors but is absent ...Eukaryotic ribosome biogenesis is initiated with the transcription of pre-ribosomal RNA at the 5' external transcribed spacer, which directs the early association of assembly factors but is absent from the mature ribosome. The subsequent co-transcriptional association of ribosome assembly factors with pre-ribosomal RNA results in the formation of the small subunit processome. Here we show that stable rRNA domains of the small ribosomal subunit can independently recruit their own biogenesis factors in vivo. The final assembly and compaction of the small subunit processome requires the presence of the 5' external transcribed spacer RNA and all ribosomal RNA domains. Additionally, our cryo-electron microscopy structure of the earliest nucleolar pre-ribosomal assembly - the 5' external transcribed spacer ribonucleoprotein - provides a mechanism for how conformational changes in multi-protein complexes can be employed to regulate the accessibility of binding sites and therefore define the chronology of maturation events during early stages of ribosome assembly. | |||||||||
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_0441.map.gz | 10.9 MB | EMDB map data format | |
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Header (meta data) | emd-0441-v30.xml emd-0441.xml | 57 KB 57 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0441_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_0441.png | 179.5 KB | ||
Filedesc metadata | emd-0441.cif.gz | 15.9 KB | ||
Others | emd_0441_additional.map.gz | 140.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0441 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0441 | HTTPS FTP |
-Validation report
Summary document | emd_0441_validation.pdf.gz | 395.5 KB | Display | EMDB validaton report |
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Full document | emd_0441_full_validation.pdf.gz | 395 KB | Display | |
Data in XML | emd_0441_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_0441_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0441 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0441 | HTTPS FTP |
-Related structure data
Related structure data | 6nd4MC 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_0441.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | masked, sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: unsharpened map
File | emd_0441_additional.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 5' ETS particle
+Supramolecule #1: 5' ETS particle
+Macromolecule #1: 5'ETS rRNA
+Macromolecule #2: 18S rRNA 5' domain start
+Macromolecule #3: U3 snoRNA
+Macromolecule #4: Utp17
+Macromolecule #5: Utp8
+Macromolecule #6: Utp15
+Macromolecule #7: Utp9
+Macromolecule #8: Utp5
+Macromolecule #9: Utp10
+Macromolecule #10: Utp4
+Macromolecule #11: Utp1
+Macromolecule #12: Utp6
+Macromolecule #13: Utp12
+Macromolecule #14: Utp13
+Macromolecule #15: Utp18
+Macromolecule #16: Utp21
+Macromolecule #17: Sof1
+Macromolecule #18: Utp7
+Macromolecule #19: Imp3
+Macromolecule #20: Mpp10
+Macromolecule #21: Bud21
+Macromolecule #22: Nop56
+Macromolecule #23: Nop58
+Macromolecule #24: Nop1.1
+Macromolecule #25: Snu13
+Macromolecule #26: Rrp9
+Macromolecule #27: Utp24
+Macromolecule #28: Unidentified fragment
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.7 Component:
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Grid | Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: LACEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-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: 1 / Number real images: 2750 / Average exposure time: 0.25 sec. / Average electron dose: 31.25 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: 3.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |