[English] 日本語
Yorodumi- EMDB-24296: State E1 nucleolar 60S ribosome biogenesis intermediate - Composi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24296 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model | ||||||||||||
Map data | State E1 Overall map | ||||||||||||
Sample |
| ||||||||||||
Function / homology | Function and homology information 25S rRNA (cytosine2870-C5)-methyltransferase / Noc1p-Noc2p complex / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / Noc2p-Noc3p complex / snoRNA release from pre-rRNA / rRNA (guanosine-2'-O-)-methyltransferase activity / nuclear division / 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 / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...25S rRNA (cytosine2870-C5)-methyltransferase / Noc1p-Noc2p complex / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / Noc2p-Noc3p complex / snoRNA release from pre-rRNA / rRNA (guanosine-2'-O-)-methyltransferase activity / nuclear division / 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 / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (cytosine-C5-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / intracellular mRNA localization / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / PeBoW complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear pre-replicative complex / rRNA base methylation / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / positive regulation of ATP-dependent activity / protein folding chaperone complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / nuclear-transcribed mRNA catabolic process / 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) / maturation of 5.8S rRNA / proteasome binding / ribosomal subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / ATPase activator activity / Formation of a pool of free 40S subunits / ribosomal large subunit binding / 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 / ribosomal large subunit export from nucleus / mRNA transport / 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) / regulation of translational fidelity / ribonucleoprotein complex binding / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translation initiation factor activity / nuclear periphery / small-subunit processome / proteasome complex / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / maintenance of translational fidelity / macroautophagy / protein catabolic process / ribosomal small subunit biogenesis / ribosomal large subunit assembly / rRNA processing / large ribosomal subunit rRNA binding / protein-macromolecule adaptor activity / protein transport / large ribosomal subunit / ribosome biogenesis / nuclear envelope / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / ATPase binding / negative regulation of translation / RNA helicase activity / rRNA binding / RNA helicase / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cell division / mRNA binding / GTPase activity / chromatin binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / metal ion binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae BY4741 (yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||||||||
Authors | Cruz VE / Sekulski K / Peddada N / Erzberger JP | ||||||||||||
Funding support | United States, 3 items
| ||||||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_24296.map.gz | 249.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-24296-v30.xml emd-24296.xml | 84.3 KB 84.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_24296_fsc.xml | 14.9 KB | Display | FSC data file |
Images | emd_24296.png | 169.5 KB | ||
Others | emd_24296_half_map_1.map.gz emd_24296_half_map_2.map.gz | 239.6 MB 239.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24296 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24296 | HTTPS FTP |
-Related structure data
Related structure data | 7r7aMC 7nacC 7nadC 7nafC 7r6kC 7r6qC 7r72C 7r7cC 7u0hC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_24296.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | State E1 Overall map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: State E1 Overall half map 2
File | emd_24296_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | State E1 Overall half map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: State E1 Overall half map 1
File | emd_24296_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | State E1 Overall half map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
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 #52: 5.8S ribosomal RNA gene and internal transcribed spacer 2
+Macromolecule #3: 60S ribosomal subunit assembly/export protein LOC1
+Macromolecule #4: Ribosome biogenesis protein BRX1
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4-A
+Macromolecule #7: 60S ribosomal protein L6-A
+Macromolecule #8: 60S ribosomal protein L7-A
+Macromolecule #9: 60S ribosomal protein L9-A
+Macromolecule #10: rRNA-processing protein EBP2
+Macromolecule #11: 60S ribosomal protein L13-A
+Macromolecule #12: 60S ribosomal protein L14-A
+Macromolecule #13: 60S ribosomal protein L15-A
+Macromolecule #14: 60S ribosomal protein L16-A
+Macromolecule #15: 60S ribosomal protein L17-A
+Macromolecule #16: 60S ribosomal protein L18-A
+Macromolecule #17: 60S ribosomal protein L20-A
+Macromolecule #18: 60S ribosomal protein L21-A
+Macromolecule #19: Ribosome assembly factor MRT4
+Macromolecule #20: 60S ribosomal protein L25
+Macromolecule #21: 60S ribosomal protein L26-A
+Macromolecule #22: Nucleolar GTP-binding protein 1
+Macromolecule #23: 60S ribosomal protein L31-A
+Macromolecule #24: 60S ribosomal protein L32
+Macromolecule #25: 60S ribosomal protein L33-A
+Macromolecule #26: 60S ribosomal protein L35-A
+Macromolecule #27: 60S ribosomal protein L36-A
+Macromolecule #28: 60S ribosomal protein L37-A
+Macromolecule #29: 60S ribosome subunit biogenesis protein NIP7
+Macromolecule #30: Ribosome biogenesis protein ERB1
+Macromolecule #31: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
+Macromolecule #32: Ribosome biogenesis protein NSA2
+Macromolecule #33: Nuclear GTP-binding protein NUG1
+Macromolecule #34: Ribosome biogenesis protein RLP24
+Macromolecule #35: Nucleolar protein 16
+Macromolecule #36: Eukaryotic translation initiation factor 6
+Macromolecule #37: UPF0642 protein YBL028C
+Macromolecule #38: Nucleolar complex protein 2
+Macromolecule #39: Nucleolar complex-associated protein 3
+Macromolecule #40: Proteasome-interacting protein CIC1
+Macromolecule #41: 60S ribosomal protein L23-A
+Macromolecule #42: 60S ribosomal protein L19-A
+Macromolecule #43: 60S ribosomal protein L8-A
+Macromolecule #44: 60S ribosomal protein L27-A
+Macromolecule #45: 60S ribosomal protein L22-A
+Macromolecule #46: 60S ribosomal protein L30
+Macromolecule #47: 60S ribosomal protein L34-A
+Macromolecule #48: 60S ribosomal protein L38
+Macromolecule #49: Pescadillo homolog
+Macromolecule #50: YTM1 isoform 1
+Macromolecule #51: Ribosome biogenesis protein RLP7
+Macromolecule #53: ATP-dependent RNA helicase HAS1
+Macromolecule #54: Ribosome biogenesis protein 15
+Macromolecule #55: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+Macromolecule #56: Ribosomal protein
+Macromolecule #57: ATP-dependent rRNA helicase SPB4
+Macromolecule #58: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.45 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| ||||||||||||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.30000000000000004 nm / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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: 0.9 µm / Nominal defocus min: 0.2 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 |
---|---|
Output model | PDB-7r7a: |