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Yorodumi- EMDB-35279: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35279 | |||||||||
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Title | Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Mak16 | |||||||||
Map data | local resolution filtered map | |||||||||
Sample |
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Keywords | Ribosome / Ribosome biogenesis / pre-60S ribosome | |||||||||
Function / homology | Function and homology information dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / PeBoW complex / rRNA primary transcript binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / maturation of 5.8S rRNA / preribosome, large subunit precursor / 90S preribosome ...dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / PeBoW complex / rRNA primary transcript binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / maturation of 5.8S rRNA / preribosome, large subunit precursor / 90S preribosome / post-translational protein modification / ribonucleoprotein complex binding / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / ribosomal large subunit biogenesis / rRNA processing / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / negative regulation of translation / ribosome / RNA helicase / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / nucleolus / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Lau B / Huang Z / Beckmann R / Hurt E / Cheng J | |||||||||
Funding support | 1 items
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Citation | Journal: EMBO Rep / Year: 2023 Title: Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis. Authors: Benjamin Lau / Zixuan Huang / Nikola Kellner / Shuangshuang Niu / Otto Berninghausen / Roland Beckmann / Ed Hurt / Jingdong Cheng / Abstract: Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ...Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35279.map.gz | 163.6 MB | EMDB map data format | |
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Header (meta data) | emd-35279-v30.xml emd-35279.xml | 61.3 KB 61.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35279_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_35279.png | 88 KB | ||
Filedesc metadata | emd-35279.cif.gz | 14 KB | ||
Others | emd_35279_additional_1.map.gz emd_35279_half_map_1.map.gz emd_35279_half_map_2.map.gz | 246.6 MB 225.1 MB 225 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35279 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35279 | HTTPS FTP |
-Validation report
Summary document | emd_35279_validation.pdf.gz | 828.7 KB | Display | EMDB validaton report |
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Full document | emd_35279_full_validation.pdf.gz | 828.2 KB | Display | |
Data in XML | emd_35279_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | emd_35279_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35279 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35279 | HTTPS FTP |
-Related structure data
Related structure data | 8i9pMC 8i9rC 8i9tC 8i9vC 8i9wC 8i9xC 8i9yC 8i9zC 8ia0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_35279.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | local resolution filtered map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.045 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: cry-em map filtered by DeepEMhancer
File | emd_35279_additional_1.map | ||||||||||||
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Annotation | cry-em map filtered by DeepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35279_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35279_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : pre-60S ribosome
+Supramolecule #1: pre-60S ribosome
+Supramolecule #2: ribosome
+Macromolecule #1: RNA (3341-MER)
+Macromolecule #2: RNA (306-MER)
+Macromolecule #3: Brix domain-containing protein
+Macromolecule #4: Ribosome biogenesis protein C8F11.04
+Macromolecule #5: Ribosome biogenesis protein ERB1
+Macromolecule #6: RNA helicase
+Macromolecule #7: Putative RNA-binding protein
+Macromolecule #8: Pescadillo homolog
+Macromolecule #9: 60S ribosomal protein l7-like protein
+Macromolecule #10: Nucleolar protein 16
+Macromolecule #11: rRNA-processing protein EBP2
+Macromolecule #12: 60S ribosomal protein L4-like protein
+Macromolecule #13: 60S ribosomal protein L6
+Macromolecule #14: 60S ribosomal protein L8
+Macromolecule #15: 60S ribosomal protein L13
+Macromolecule #16: 60S ribosomal protein L14-like protein
+Macromolecule #17: Ribosomal protein L15
+Macromolecule #18: 60S ribosomal protein L16-like protein
+Macromolecule #19: 60S ribosomal protein l17-like protein
+Macromolecule #20: Ribosomal protein L18-like protein
+Macromolecule #21: 60S ribosomal protein L20
+Macromolecule #22: 60S ribosomal protein l21-like protein
+Macromolecule #23: 60S ribosomal protein L25-like protein
+Macromolecule #24: 60S ribosomal protein L26-like protein
+Macromolecule #25: 60S ribosomal protein L32-like protein
+Macromolecule #26: 60S ribosomal protein l33-like protein
+Macromolecule #27: dolichyl-diphosphooligosaccharide--protein glycotransferase
+Macromolecule #28: 60S ribosomal protein L36
+Macromolecule #29: Ribosomal protein L37
+Macromolecule #30: Ribosomal RNA-processing protein 1
+Macromolecule #31: Brix domain-containing protein
+Macromolecule #32: Protein MAK16
+Macromolecule #33: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |