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Yorodumi- EMDB-24286: State E2 nucleolar 60S ribosome biogenesis intermediate - Foot re... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24286 | ||||||||||||
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Title | State E2 nucleolar 60S ribosome biogenesis intermediate - Foot region map | ||||||||||||
Map data | State E2 foot region locally refined map | ||||||||||||
Sample |
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Keywords | ribosome biogenesis / DEAD-box ATPase / methyltransferase / nucleolus / RIBOSOME | ||||||||||||
Function / homology | Function and homology information snoRNA release from pre-rRNA / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome binding / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit ...snoRNA release from pre-rRNA / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / proteasome binding / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 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 / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / ribonucleoprotein complex binding / maturation of LSU-rRNA / proteasome complex / maturation of 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) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / protein catabolic process / rRNA processing / ribosomal small subunit biogenesis / ribosomal large subunit assembly / nuclear envelope / protein-macromolecule adaptor activity / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / RNA helicase / structural constituent of ribosome / mRNA binding / nucleolus / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae BY4741 (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.98 Å | ||||||||||||
Authors | Cruz VE / Sekulski K / Peddada N / Erzberger JP | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. Authors: Victor Emmanuel Cruz / Kamil Sekulski / Nagesh Peddada / Carolin Sailer / Sahana Balasubramanian / Christine S Weirich / Florian Stengel / Jan P Erzberger / Abstract: DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular ...DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24286.map.gz | 253.5 MB | EMDB map data format | |
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Header (meta data) | emd-24286-v30.xml emd-24286.xml | 38.9 KB 38.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24286_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_24286.png | 139.3 KB | ||
Filedesc metadata | emd-24286.cif.gz | 9.6 KB | ||
Others | emd_24286_half_map_1.map.gz emd_24286_half_map_2.map.gz | 243 MB 242.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24286 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24286 | HTTPS FTP |
-Validation report
Summary document | emd_24286_validation.pdf.gz | 908.9 KB | Display | EMDB validaton report |
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Full document | emd_24286_full_validation.pdf.gz | 908.4 KB | Display | |
Data in XML | emd_24286_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | emd_24286_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24286 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24286 | HTTPS FTP |
-Related structure data
Related structure data | 7r6qMC 7nacC 7nadC 7nafC 7r6kC 7r72C 7r7aC 7r7cC 7u0hC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24286.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | State E2 foot region locally refined map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: State E2 foot region locally refined half map 1
File | emd_24286_half_map_1.map | ||||||||||||
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Annotation | State E2 foot region locally refined half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: State E2 foot region locally refined half map 2
File | emd_24286_half_map_2.map | ||||||||||||
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Annotation | State E2 foot region locally refined half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4
+Supramolecule #1: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4
+Macromolecule #1: ITS-2
+Macromolecule #10: 25S rRNA
+Macromolecule #12: 5.8S rRNA
+Macromolecule #2: ATP-dependent RNA helicase HAS1
+Macromolecule #3: 60S ribosomal protein L8-A
+Macromolecule #4: Proteasome-interacting protein CIC1
+Macromolecule #5: Pescadillo homolog
+Macromolecule #6: Ribosome biogenesis protein 15
+Macromolecule #7: Ribosome biogenesis protein RLP7
+Macromolecule #8: 60S ribosomal protein L25
+Macromolecule #9: Ribosome biogenesis protein ERB1
+Macromolecule #11: Nucleolar protein 16
+Macromolecule #13: 60S ribosomal protein L15-A
+Macromolecule #14: 60S ribosomal protein L35
+Macromolecule #15: 60S ribosomal protein L27
+Macromolecule #16: 60S ribosomal protein L34-A
+Macromolecule #17: 60S ribosome biogenesis factor Spb1
+Macromolecule #18: 60S ribosomal protein L36-A
+Macromolecule #19: 60S ribosomal protein L13-A
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.45 mg/mL | ||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.3 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4523 / Average exposure time: 0.05 sec. / Average electron dose: 1.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |