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- EMDB-24271: State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-M... -
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Open data
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Basic information
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Title | State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD locally refined map | ||||||||||||
![]() | State E2 Spb1-MTD locally refined map | ||||||||||||
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![]() | ribosome biogenesis / DEAD-box ATPases / methyltransferase / nucleolus / RIBOSOME | ||||||||||||
Function / homology | ![]() 25S rRNA (cytosine2870-C5)-methyltransferase / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / tRNA methylation ...25S rRNA (cytosine2870-C5)-methyltransferase / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / tRNA methylation / rRNA base methylation / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / maturation of 5.8S rRNA / 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 / ribosomal large subunit binding / 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) / ATPase activator activity / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / regulation of translational fidelity / ribosomal subunit export from nucleus / translation initiation factor activity / 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 / cytosolic ribosome assembly / ribosomal large subunit biogenesis / maintenance of translational fidelity / ribosomal large subunit assembly / rRNA processing / transcription corepressor activity / protein transport / histone binding / ATPase binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / translation / GTPase activity / mRNA binding / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / mitochondrion / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.13 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) | ![]() ![]() | 34.5 KB 34.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 84.9 KB | ||
Filedesc metadata | ![]() | 8.2 KB | ||
Others | ![]() ![]() | 242.6 MB 242.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 877.3 KB | Display | ![]() |
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Full document | ![]() | 876.9 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nafMC ![]() 7nacC ![]() 7nadC ![]() 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 Spb1-MTD 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 E2 Spb1-MTD locally refined half map 2
File | emd_24271_half_map_1.map | ||||||||||||
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Annotation | State E2 Spb1-MTD locally refined half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: State E2 Spb1-MTD locally refined half map 1
File | emd_24271_half_map_2.map | ||||||||||||
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Annotation | State E2 Spb1-MTD 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: Ribosomal RNA-processing protein 17
+Macromolecule #3: Nucleolar complex protein 2
+Macromolecule #4: 60S ribosomal protein L23-A
+Macromolecule #5: Ribosome biogenesis protein RLP24
+Macromolecule #6: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+Macromolecule #7: 60S ribosome biogenesis factor Nog1
+Macromolecule #8: 60S ribosomal protein L31-A
+Macromolecule #9: 60S ribosomal protein L22-A
+Macromolecule #10: 60S ribosome ribosomal protein L19A
+Macromolecule #11: 60S ribosomal protein L30
+Macromolecule #12: 60S ribosomal protein L3
+Macromolecule #13: UPF0642 protein YBL028C
+Macromolecule #14: Nuclear GTP-binding protein NUG1
+Macromolecule #15: Eukaryotic translation initiation factor 6
+Macromolecule #16: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
+Macromolecule #17: S-ADENOSYL-L-HOMOCYSTEINE
+Macromolecule #18: water
-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-7naf: |