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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 RNA fragment catabolic process / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / t-UTP complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA modification / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis ...RNA fragment catabolic process / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / t-UTP complex / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA modification / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / septum digestion after cytokinesis / snRNA binding / box C/D sno(s)RNA 3'-end processing / positive regulation of RNA binding / regulation of transcription by RNA polymerase I / rDNA heterochromatin / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / tRNA export from nucleus / rRNA methyltransferase activity / SUMOylation of RNA binding proteins / positive regulation of rRNA processing / box C/D methylation guide snoRNP complex / U4/U6 snRNP / sno(s)RNA-containing ribonucleoprotein complex / O-methyltransferase activity / protein localization to nucleolus / U4 snRNA binding / rRNA methylation / U4 snRNP / U3 snoRNA binding / preribosome, small subunit precursor / establishment of cell polarity / snoRNA binding / precatalytic spliceosome / spliceosomal complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of transcription by RNA polymerase I / 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) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA endonuclease activity / U4/U6 x U5 tri-snRNP complex / maturation of SSU-rRNA / maturation of LSU-rRNA / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / spliceosomal complex / rRNA processing / mRNA splicing, via spliceosome / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / 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 |
-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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |