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Yorodumi- EMDB-35285: Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35285 | |||||||||
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Title | Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-2 | |||||||||
Map data | local resolution filtered map | |||||||||
Sample |
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Keywords | Ribosome / Ribosome biogenesis / pre-60S ribosome | |||||||||
Function / homology | Function and homology information Noc1p-Noc2p complex / Noc2p-Noc3p complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / intracellular mRNA localization / protein N-linked glycosylation via asparagine ...Noc1p-Noc2p complex / Noc2p-Noc3p complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / tRNA (cytidine-5-)-methyltransferase activity / intracellular mRNA localization / protein N-linked glycosylation via asparagine / PeBoW complex / tRNA methylation / rRNA primary transcript binding / rRNA base methylation / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process / preribosome, small subunit precursor / maturation of 5.8S rRNA / ribosomal large subunit binding / preribosome, large subunit precursor / DNA replication initiation / mRNA transport / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / translation initiation factor activity / ribosome assembly / nuclear periphery / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / post-translational protein modification / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / cytosolic ribosome assembly / ribosomal large subunit biogenesis / rRNA processing / transcription corepressor activity / ribosome biogenesis / ribosomal small subunit biogenesis / histone binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / rRNA binding / negative regulation of translation / ribosome / RNA helicase / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / chromatin binding / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 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_35285.map.gz | 163.5 MB | EMDB map data format | |
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Header (meta data) | emd-35285-v30.xml emd-35285.xml | 92.4 KB 92.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35285_fsc.xml | 14.9 KB | Display | FSC data file |
Images | emd_35285.png | 128.6 KB | ||
Filedesc metadata | emd-35285.cif.gz | 20.7 KB | ||
Others | emd_35285_additional_1.map.gz emd_35285_half_map_1.map.gz emd_35285_half_map_2.map.gz | 246.8 MB 225.4 MB 225.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35285 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35285 | HTTPS FTP |
-Validation report
Summary document | emd_35285_validation.pdf.gz | 953 KB | Display | EMDB validaton report |
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Full document | emd_35285_full_validation.pdf.gz | 952.6 KB | Display | |
Data in XML | emd_35285_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | emd_35285_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35285 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35285 | HTTPS FTP |
-Related structure data
Related structure data | 8i9vMC 8i9pC 8i9rC 8i9tC 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_35285.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: DeepEMhancer filtered map
File | emd_35285_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35285_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35285_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 (256-MER)
+Macromolecule #3: RNA (161-MER)
+Macromolecule #4: Brix domain-containing protein
+Macromolecule #5: Ribosome biogenesis protein C8F11.04
+Macromolecule #6: Ribosome biogenesis protein ERB1
+Macromolecule #7: RNA helicase
+Macromolecule #8: Ribosome assembly factor mrt4
+Macromolecule #9: 60S ribosome subunit biogenesis protein NIP7
+Macromolecule #10: Nucleolar GTP-binding protein 1
+Macromolecule #11: Putative RNA-binding protein
+Macromolecule #12: Pescadillo homolog
+Macromolecule #13: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #14: Putative GTP binding protein
+Macromolecule #15: 60S ribosomal protein l7-like protein
+Macromolecule #16: Eukaryotic translation initiation factor 6
+Macromolecule #17: DUF2423 domain-containing protein
+Macromolecule #18: RNA methyltransferase nop2-like protein
+Macromolecule #19: Ribosome biogenesis protein RLP24
+Macromolecule #20: Nucleolar protein 16
+Macromolecule #21: AdoMet-dependent rRNA methyltransferase SPB1
+Macromolecule #22: Nucleolar complex-associated protein 3
+Macromolecule #23: rRNA-processing protein EBP2
+Macromolecule #24: 60S ribosomal subunit-like protein
+Macromolecule #25: Putative NOC2 family protein
+Macromolecule #26: rRNA-processing protein
+Macromolecule #27: ATP-dependent RNA helicase DBP10
+Macromolecule #28: 60S ribosomal protein L3-like protein
+Macromolecule #29: 60S ribosomal protein L4-like protein
+Macromolecule #30: 60S ribosomal protein L6
+Macromolecule #31: 60S ribosomal protein L8
+Macromolecule #32: 60S ribosomal protein l9-like protein
+Macromolecule #33: 60S ribosomal protein L12-like protein
+Macromolecule #34: 60S ribosomal protein L13
+Macromolecule #35: 60S ribosomal protein L14-like protein
+Macromolecule #36: Ribosomal protein L15
+Macromolecule #37: 60S ribosomal protein L16-like protein
+Macromolecule #38: 60S ribosomal protein l17-like protein
+Macromolecule #39: Ribosomal protein L18-like protein
+Macromolecule #40: 60S ribosomal protein L20
+Macromolecule #41: 60S ribosomal protein l21-like protein
+Macromolecule #42: 60S ribosomal protein l23-like protein
+Macromolecule #43: 60S ribosomal protein L25-like protein
+Macromolecule #44: 60S ribosomal protein L26-like protein
+Macromolecule #45: Putative 60S ribosomal protein
+Macromolecule #46: 60S ribosomal protein L32-like protein
+Macromolecule #47: 60S ribosomal protein l33-like protein
+Macromolecule #48: dolichyl-diphosphooligosaccharide--protein glycotransferase
+Macromolecule #49: 60S ribosomal protein L36
+Macromolecule #50: Ribosomal protein L37
+Macromolecule #51: Ribosomal protein
+Macromolecule #52: Ribosomal RNA-processing protein 1
+Macromolecule #53: Brix domain-containing protein
+Macromolecule #54: Protein MAK16
+Macromolecule #55: 60S ribosome biogenesis protein Rrp14
+Macromolecule #56: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #57: 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 |