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- 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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![]() | Pre-60S ribosomal subunit / Assembly intermediate / Ribosome / Nucleoprotein complex | |||||||||
Function / homology | ![]() inner cell mass cell differentiation / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / hematopoietic stem cell homeostasis / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation ...inner cell mass cell differentiation / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / hematopoietic stem cell homeostasis / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / stem cell division / miRNA-mediated gene silencing by inhibition of translation / negative regulation of protein neddylation / positive regulation of telomere maintenance / negative regulation of formation of translation preinitiation complex / ribosomal protein import into nucleus / protein localization to nucleolus / GAIT complex / skeletal system morphogenesis / regulation of reactive oxygen species metabolic process / regulation of glycolytic process / regulation of G1 to G0 transition / nuclear-transcribed mRNA catabolic process / protein-DNA complex disassembly / negative regulation of ubiquitin protein ligase activity / mitotic metaphase chromosome alignment / stem cell population maintenance / regulation of cyclin-dependent protein serine/threonine kinase activity / G1 to G0 transition / homeostatic process / positive regulation of dendritic spine development / negative regulation of cell-cell adhesion / lung morphogenesis / negative regulation of DNA replication / maturation of 5.8S rRNA / macrophage chemotaxis / Peptide chain elongation / ribosomal large subunit binding / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / preribosome, large subunit precursor / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / protein localization to nucleus / negative regulation of mitotic cell cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein targeting / cellular response to interleukin-4 / hematopoietic progenitor cell differentiation / cellular response to actinomycin D / somitogenesis / ribosomal subunit export from nucleus / cytosolic ribosome / rough endoplasmic reticulum / 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) / Notch signaling pathway / negative regulation of protein ubiquitination / translation initiation factor activity / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of cell migration / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / maturation of LSU-rRNA / condensed nuclear chromosome / regulation of signal transduction by p53 class mediator / ribosomal large subunit biogenesis / kidney development / mRNA 3'-UTR binding / positive regulation of translation / response to insulin / ribosomal large subunit assembly / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / positive regulation of miRNA transcription / cellular response to type II interferon / osteoblast differentiation / rRNA processing / large ribosomal subunit / positive regulation of canonical Wnt signaling pathway / ribosome biogenesis / positive regulation of protein binding / ribosome binding / chromosome / mitotic cell cycle / regulation of cell population proliferation / midbody Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.91 Å | |||||||||
![]() | Vanden Broeck A / Klinge S | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: 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. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 37.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 57 KB 57 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.9 KB | Display | ![]() |
Images | ![]() | 133.6 KB | ||
Masks | ![]() | 421.9 MB | ![]() | |
Filedesc metadata | ![]() | 14.6 KB | ||
Others | ![]() ![]() | 390.9 MB 390.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | 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 ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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Projections & Slices |
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Density Histograms |
-Half map: #2
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Projections & Slices |
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Density Histograms |
-Half map: #1
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Projections & Slices |
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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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![]() | 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: ![]() |
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: |