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Yorodumi- EMDB-24290: State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 lo... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24290 | ||||||||||||
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Title | State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 locally refined map | ||||||||||||
Map data | State E1 Spb4 locally refined map | ||||||||||||
Sample |
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Function / homology | Function and homology information Noc1p-Noc2p complex / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / Noc2p-Noc3p complex / rRNA (guanosine-2'-O-)-methyltransferase activity / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear pre-replicative complex / rRNA primary transcript binding ...Noc1p-Noc2p complex / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / Noc2p-Noc3p complex / rRNA (guanosine-2'-O-)-methyltransferase activity / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear pre-replicative complex / rRNA primary transcript binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ATPase activator activity / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / DNA replication initiation / regulation of translational fidelity / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / assembly of large subunit precursor of preribosome / maintenance of translational fidelity / ribosomal large subunit assembly / rRNA processing / ribosome biogenesis / cytoplasmic translation / cytosolic large ribosomal subunit / ATPase binding / RNA helicase activity / rRNA binding / RNA helicase / structural constituent of ribosome / translation / cell division / mRNA binding / GTPase activity / chromatin binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae BY4741 (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.07 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_24290.map.gz | 254.4 MB | EMDB map data format | |
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Header (meta data) | emd-24290-v30.xml emd-24290.xml | 46 KB 46 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24290_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_24290.png | 132 KB | ||
Others | emd_24290_half_map_1.map.gz emd_24290_half_map_2.map.gz | 251.2 MB 246.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24290 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24290 | HTTPS FTP |
-Related structure data
Related structure data | 7r72MC 7nacC 7nadC 7nafC 7r6kC 7r6qC 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_24290.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | State E1 Spb4 locally refined map | ||||||||||||||||||||
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 E1 Spb4 locally refined half map 2
File | emd_24290_half_map_1.map | ||||||||||||
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Annotation | State E1 Spb4 locally refined half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: State E1 Spb4 locally refined half map 1
File | emd_24290_half_map_2.map | ||||||||||||
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Annotation | State E1 Spb4 locally refined half map 1 | ||||||||||||
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: 25S rRNA
+Macromolecule #2: 5.8S rRNA
+Macromolecule #3: Nucleolar complex protein 2
+Macromolecule #4: 60S ribosomal protein L3
+Macromolecule #5: 60S ribosomal protein L8-A
+Macromolecule #6: Nucleolar complex-associated protein 3
+Macromolecule #7: 60S ribosomal protein L17-A
+Macromolecule #8: 60S ribosomal protein L19-A
+Macromolecule #9: 60S ribosomal protein L22-A
+Macromolecule #10: 60S ribosomal protein L25
+Macromolecule #11: 60S ribosomal protein L27-A
+Macromolecule #12: Nucleolar GTP-binding protein 1
+Macromolecule #13: 60S ribosomal protein L30
+Macromolecule #14: 60S ribosomal protein L31-A
+Macromolecule #15: 60S ribosomal protein L34-A
+Macromolecule #16: 60S ribosomal protein L37-A
+Macromolecule #17: 60S ribosomal protein L38
+Macromolecule #18: Ribosome biogenesis protein ERB1
+Macromolecule #19: Pescadillo homolog
+Macromolecule #20: Ribosome biogenesis protein YTM1
+Macromolecule #21: Ribosome biogenesis protein RLP7
+Macromolecule #22: Ribosome biogenesis protein RLP24
+Macromolecule #23: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+Macromolecule #24: ATP-dependent rRNA helicase SPB4
+Macromolecule #25: ZINC ION
-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: 0.30000000000000004 nm | ||||||||||||||||||
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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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 FIELDBright-field microscopy / 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 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-7r72: |