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- EMDB-24290: State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 lo... -
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Open data
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Basic information
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Title | State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 locally refined map | ||||||||||||
![]() | State E1 Spb4 locally refined map | ||||||||||||
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![]() | ribosome biogenesis / DEAD-box ATPases / methyltransferase / nucleolus / RIBOSOME | ||||||||||||
Function / homology | ![]() 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / 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 / PeBoW complex / nuclear pre-replicative complex ...27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / 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 / PeBoW complex / 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) / 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 / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / DNA replication initiation / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / 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 / ATPase binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / RNA helicase / structural constituent of ribosome / translation / cell division / GTPase activity / mRNA binding / chromatin binding / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.07 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 | ![]() | 254.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 47.5 KB 47.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.8 KB | Display | ![]() |
Images | ![]() | 132 KB | ||
Filedesc metadata | ![]() | 11.9 KB | ||
Others | ![]() ![]() | 251.2 MB 246.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 925.5 KB | Display | ![]() |
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Full document | ![]() | 925 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r72MC ![]() 7nacC ![]() 7nadC ![]() 7nafC ![]() 7r6kC ![]() 7r6qC ![]() 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
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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 |
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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: 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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![]() | 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 | ||||||||||||||||||
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-7r72: |