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Yorodumi- EMDB-29263: Human nucleolar pre-60S ribosomal subunit (State H) - Composite map -
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Open data
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Basic information
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| Title | Human nucleolar pre-60S ribosomal subunit (State H) - Composite map | |||||||||
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Sample |
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Keywords | Pre-60S ribosomal subunit / Assembly intermediate / Ribosome / Nucleoprotein complex | |||||||||
| Function / homology | Function and homology informationpositive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / dendrite extension / inner cell mass cell differentiation / preribosome binding / hematopoietic stem cell homeostasis / lamin filament / regulation of fatty acid biosynthetic process / regulation of Notch signaling pathway / regulation of megakaryocyte differentiation ...positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / dendrite extension / inner cell mass cell differentiation / preribosome binding / hematopoietic stem cell homeostasis / lamin filament / regulation of fatty acid biosynthetic process / regulation of Notch signaling pathway / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / negative regulation of G2/M transition of mitotic cell cycle / positive regulation of protein sumoylation / miRNA-mediated gene silencing by inhibition of translation / negative regulation of protein neddylation / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / protein localization to nucleolus / ribosomal protein import into nucleus / negative regulation of mitotic cell cycle / protein-DNA complex disassembly / GAIT complex / regulation of glycolytic process / G1 to G0 transition / skeletal system morphogenesis / regulation of reactive oxygen species metabolic process / negative regulation of cell-cell adhesion / maturation of 5.8S rRNA / stem cell division / mitotic metaphase chromosome alignment / stem cell population maintenance / negative regulation of ubiquitin protein ligase activity / homeostatic process / negative regulation of DNA replication / positive regulation of dendritic spine development / macrophage chemotaxis / ribosomal large subunit binding / lung morphogenesis / positive regulation of telomere maintenance / positive regulation of natural killer cell proliferation / preribosome, large subunit precursor / nuclear-transcribed mRNA catabolic process / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / cellular response to actinomycin D / Eukaryotic Translation Termination / negative regulation of ubiquitin-dependent protein catabolic process / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / Viral mRNA Translation / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / somitogenesis / positive regulation of protein binding / L13a-mediated translational silencing of Ceruloplasmin expression / hematopoietic progenitor cell differentiation / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / ribosomal subunit export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / Notch signaling pathway / 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) / rough endoplasmic reticulum / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / translation initiation factor activity / negative regulation of protein ubiquitination / cytosolic ribosome / cellular response to interleukin-4 / negative regulation of cell migration / assembly of large subunit precursor of preribosome / regulation of signal transduction by p53 class mediator / positive regulation of translation / cytosolic ribosome assembly / ribosomal large subunit biogenesis / condensed nuclear chromosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA 3'-UTR binding / kidney development / response to insulin / mRNA 5'-UTR binding / positive regulation of miRNA transcription / cellular response to type II interferon / transcription coactivator binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / osteoblast differentiation / positive regulation of canonical Wnt signaling pathway / mitotic cell cycle / regulation of cell population proliferation / large ribosomal subunit / ribosome biogenesis / chromosome / ribosome binding / cell body Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.91 Å | |||||||||
Authors | Vanden Broeck A / Klinge S | |||||||||
| Funding support | European Union, United States, 2 items
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Citation | Journal: Science / Year: 2023Title: Principles of human pre-60 biogenesis. Authors: Arnaud Vanden Broeck / Sebastian Klinge / ![]() Abstract: During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an ...During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60 assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60 particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_29263.map.gz | 37.9 MB | EMDB map data format | |
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| Header (meta data) | emd-29263-v30.xml emd-29263.xml | 57 KB 57 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_29263_fsc.xml | 15.9 KB | Display | FSC data file |
| Images | emd_29263.png | 133.6 KB | ||
| Masks | emd_29263_msk_1.map | 421.9 MB | Mask map | |
| Filedesc metadata | emd-29263.cif.gz | 14.6 KB | ||
| Others | emd_29263_half_map_1.map.gz emd_29263_half_map_2.map.gz | 390.9 MB 390.9 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29263 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29263 | HTTPS FTP |
-Validation report
| Summary document | emd_29263_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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| Full document | emd_29263_full_validation.pdf.gz | 1.1 MB | Display | |
| Data in XML | emd_29263_validation.xml.gz | 25.1 KB | Display | |
| Data in CIF | emd_29263_validation.cif.gz | 32.7 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29263 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29263 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 8fl0MC ![]() 8fkpC ![]() 8fkqC ![]() 8fkrC ![]() 8fksC ![]() 8fktC ![]() 8fkuC ![]() 8fkvC ![]() 8fkwC ![]() 8fkxC ![]() 8fkyC ![]() 8fkzC ![]() 8fl2C ![]() 8fl3C ![]() 8fl4C ![]() 8fl6C ![]() 8fl7C ![]() 8fl9C ![]() 8flaC ![]() 8flbC ![]() 8flcC ![]() 8fldC ![]() 8fleC ![]() 8flfC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_29263.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.072 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_29263_msk_1.map | ||||||||||||
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| Density Histograms |
-Half map: #2
| File | emd_29263_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_29263_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : Human nucleolar pre-60S ribosomal subunit (State H)
+Supramolecule #1: Human nucleolar pre-60S ribosomal subunit (State H)
+Macromolecule #1: 60S ribosomal protein L12
+Macromolecule #4: 60S ribosomal protein L11
+Macromolecule #5: 60S ribosomal protein L13a
+Macromolecule #6: 60S ribosomal protein L14
+Macromolecule #7: 60S ribosomal protein L18
+Macromolecule #8: 60S ribosomal protein L18a
+Macromolecule #9: 60S ribosomal protein L21
+Macromolecule #10: 60S ribosomal protein L23
+Macromolecule #11: 60S ribosomal protein L28
+Macromolecule #12: 60S ribosomal protein L3
+Macromolecule #13: 60S ribosomal protein L32
+Macromolecule #14: 60S ribosomal protein L35a
+Macromolecule #15: Guanine nucleotide-binding protein-like 3
+Macromolecule #16: Nucleolar GTP-binding protein 2
+Macromolecule #17: Ribosome production factor 2 homolog
+Macromolecule #18: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #19: Notchless protein homolog 1
+Macromolecule #20: Protein LLP homolog
+Macromolecule #21: Coiled-coil domain-containing protein 86
+Macromolecule #22: 60S ribosomal protein L4
+Macromolecule #23: 60S ribosomal protein L5
+Macromolecule #24: 60S ribosomal protein L6
+Macromolecule #25: 60S ribosomal protein L7
+Macromolecule #26: 60S ribosomal protein L9
+Macromolecule #27: Eukaryotic translation initiation factor 6
+Macromolecule #28: mRNA turnover protein 4 homolog
+Macromolecule #29: GTP-binding protein 4
+Macromolecule #30: Ribosome biogenesis regulatory protein homolog
+Macromolecule #31: Probable ribosome biogenesis protein RLP24
+Macromolecule #2: 28S rRNA
+Macromolecule #3: 5S rRNA
+Macromolecule #32: MAGNESIUM ION
+Macromolecule #33: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #34: POTASSIUM ION
+Macromolecule #35: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #36: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.6 |
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| Grid | Model: Quantifoil R3.5/1 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV Details: Four applications with manual blotting before last blotting with the vitrobot.. |
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Electron microscopy
| Microscope | FEI TITAN KRIOS |
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| Specialist optics | Energy filter - Slit width: 20 eV |
| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 172699 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 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: 0.5 µm / Nominal magnification: 64000 |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
| Refinement | Space: REAL |
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| Output model | ![]() PDB-8fl0: |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
United States, 2 items
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Z (Sec.)
Y (Row.)
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FIELD EMISSION GUN

