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- EMDB-24280: State E2 nucleolar 60S ribosomal intermediate - Local Map for Noc... -
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Open data
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Basic information
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Title | State E2 nucleolar 60S ribosomal intermediate - Local Map for Noc2/Noc3 region | ||||||||||||
![]() | State E2 Noc2/Noc3 locally refined map | ||||||||||||
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![]() | ribosome biogenesis / DEAD-box ATPases / methyltransferases / 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 / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream 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 ...25S rRNA (cytosine2870-C5)-methyltransferase / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream 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 / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / intracellular mRNA localization / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / nuclear pre-replicative complex / tRNA methylation / rRNA primary transcript binding / rRNA base methylation / protein folding chaperone complex / 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 / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / DNA replication initiation / mRNA transport / ribonucleoprotein complex binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / 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 / ribosomal large subunit assembly / rRNA processing / transcription corepressor activity / ribosome biogenesis / histone binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / structural constituent of ribosome / cell division / mRNA binding / chromatin binding / nucleolus / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 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 | ![]() | 254.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 38.5 KB 38.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.9 KB | Display | ![]() |
Images | ![]() | 92.7 KB | ||
Filedesc metadata | ![]() | 10.7 KB | ||
Others | ![]() ![]() | 245.2 MB 243.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 884.7 KB | Display | ![]() |
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Full document | ![]() | 884.2 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 | ![]() 7r6kMC ![]() 7nacC ![]() 7nadC ![]() 7nafC ![]() 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 Noc2/Noc3 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 Noc2/Noc3 locally refined half map 1
File | emd_24280_half_map_1.map | ||||||||||||
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Annotation | State E2 Noc2/Noc3 locally refined half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: State E2 Noc2/Noc3 locally refined half map 2
File | emd_24280_half_map_2.map | ||||||||||||
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Annotation | State E2 Noc2/Noc3 locally refined 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: 60S ribosomal subunit assembly/export protein LOC1
+Macromolecule #3: Nucleolar complex protein 2
+Macromolecule #4: Ribosome biogenesis protein BRX1
+Macromolecule #5: 60S ribosomal protein L8-A
+Macromolecule #6: Nucleolar complex-associated protein 3
+Macromolecule #7: rRNA-processing protein EBP2
+Macromolecule #8: 60S ribosomal protein L15-A
+Macromolecule #9: 60S ribosomal protein L34-A
+Macromolecule #10: 60S ribosomal protein L36-A
+Macromolecule #11: 60S ribosome subunit biogenesis protein NIP7
+Macromolecule #12: Ribosome biogenesis protein ERB1
+Macromolecule #13: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
+Macromolecule #14: Ribosome biogenesis protein NSA2
+Macromolecule #15: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+Macromolecule #16: RRP17 isoform 1
-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 |