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- EMDB-24270: State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 l... -
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Open data
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Basic information
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Title | State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model | ||||||||||||
![]() | State E2 Spb4 map | ||||||||||||
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![]() | ribosome biogenesis / DEAD-box ATPases / methyltransferase / nucleolus / RIBOSOME | ||||||||||||
Function / homology | ![]() : / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / rRNA (uridine-2'-O-)-methyltransferase activity / PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / SRP-dependent cotranslational protein targeting to membrane ...: / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / rRNA (uridine-2'-O-)-methyltransferase activity / PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maintenance of translational fidelity / ribosomal large subunit assembly / rRNA processing / transcription corepressor activity / ribosome biogenesis / histone binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / hydrolase activity / structural constituent of ribosome / translation / GTPase activity / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||||||||
![]() | Cruz VE / Sekulski K / Peddada N / Erzberger JP | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 258.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 48.6 KB 48.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.8 KB | Display | ![]() |
Images | ![]() | 145.8 KB | ||
Filedesc metadata | ![]() | 12.1 KB | ||
Others | ![]() ![]() | 247.1 MB 247.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 926.6 KB | Display | ![]() |
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Full document | ![]() | 926.2 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nadMC ![]() 7nacC ![]() 7nafC ![]() 7r6kC ![]() 7r6qC ![]() 7r72C ![]() 7r7aC ![]() 7r7cC ![]() 7u0hC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | State E2 Spb4 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 E2 Spb4 local half map 1
File | emd_24270_half_map_1.map | ||||||||||||
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Annotation | State E2 Spb4 local half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: State E2 Spb4 local half map 2
File | emd_24270_half_map_2.map | ||||||||||||
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Annotation | State E2 Spb4 local half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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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: RRP17 isoform 1
+Macromolecule #4: NOC2 isoform 1
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: RPL8A isoform 1
+Macromolecule #7: NOC3 isoform 1
+Macromolecule #8: 60S ribosomal protein L17-A
+Macromolecule #9: 60S ribosomal protein L19-A
+Macromolecule #10: 60S ribosomal protein L22-A
+Macromolecule #11: 60S ribosomal protein L23-A
+Macromolecule #12: 60S ribosomal protein L25
+Macromolecule #13: 60S ribosomal protein L27-A
+Macromolecule #14: Nucleolar GTP-binding protein 1
+Macromolecule #15: 60S ribosomal protein L30
+Macromolecule #16: 60S ribosomal protein L31-A
+Macromolecule #17: 60S ribosomal protein L34-A
+Macromolecule #18: RPL38 isoform 1
+Macromolecule #19: Ribosome biogenesis protein ERB1
+Macromolecule #20: Pescadillo homolog
+Macromolecule #21: YTM1 isoform 1
+Macromolecule #22: RLP7 isoform 1
+Macromolecule #23: Ribosome biogenesis protein RLP24
+Macromolecule #24: SPB1 isoform 1
+Macromolecule #25: 60S ribosomal protein L37-A
+Macromolecule #26: SPB4 isoform 1
+Macromolecule #27: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7nad: |