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- EMDB-29274: Human nuclear pre-60S ribosomal subunit (State K3) - Composite map -
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Open data
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Basic information
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Title | Human nuclear pre-60S ribosomal subunit (State K3) - Composite map | |||||||||
![]() | Human nuclear pre-60S ribosomal subunit (State K3) | |||||||||
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![]() | Pre-60S ribosomal subunit / Assembly intermediate / Ribosome / Nucleoprotein complex | |||||||||
Function / homology | ![]() negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / eukaryotic 80S initiation complex ...negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / eukaryotic 80S initiation complex / miRNA-mediated gene silencing by inhibition of translation / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / negative regulation of formation of translation preinitiation complex / ribosomal protein import into nucleus / 90S preribosome assembly / TORC2 complex binding / GAIT complex / middle ear morphogenesis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / regulation of reactive oxygen species metabolic process / regulation of G1 to G0 transition / alpha-beta T cell differentiation / regulation of glycolytic process / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / nuclear-transcribed mRNA catabolic process / negative regulation of ubiquitin protein ligase activity / response to aldosterone / G1 to G0 transition / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / Protein hydroxylation / 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 / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / preribosome, large subunit precursor / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / protein localization to nucleus / 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 / protein-RNA complex assembly / 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 / cellular response to actinomycin D / cytosolic ribosome / ribosomal subunit export from nucleus / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of protein ubiquitination / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / translation initiation factor activity / embryo implantation / 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) / ossification / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / regulation of signal transduction by p53 class mediator / innate immune response in mucosa / ribosomal large subunit biogenesis / cytosolic ribosome assembly / skeletal system development / mRNA 3'-UTR binding / positive regulation of translation / sensory perception of sound / bone development / response to insulin / ribosomal large subunit assembly / cellular response to gamma radiation / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / cellular response to type II interferon / osteoblast differentiation / rRNA processing / large ribosomal subunit Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.76 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 | ![]() | 128.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 73.4 KB 73.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.8 KB | Display | ![]() |
Images | ![]() | 151.9 KB | ||
Masks | ![]() | 421.9 MB | ![]() | |
Others | ![]() ![]() | 391.2 MB 391.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 25 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8flcMC ![]() 8fkpC ![]() 8fkqC ![]() 8fkrC ![]() 8fksC ![]() 8fktC ![]() 8fkuC ![]() 8fkvC ![]() 8fkwC ![]() 8fkxC ![]() 8fkyC ![]() 8fkzC ![]() 8fl0C ![]() 8fl2C ![]() 8fl3C ![]() 8fl4C ![]() 8fl6C ![]() 8fl7C ![]() 8fl9C ![]() 8flaC ![]() 8flbC ![]() 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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Annotation | Human nuclear pre-60S ribosomal subunit (State K3) | ||||||||||||||||||||
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: Half Map 1
File | emd_29274_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map 2
File | emd_29274_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Human nuclear pre-60S ribosomal subunit (State K3)
+Supramolecule #1: Human nuclear pre-60S ribosomal subunit (State K3)
+Macromolecule #1: 60S ribosomal protein L12
+Macromolecule #5: 60S ribosomal protein L11
+Macromolecule #6: 60S ribosomal protein L13
+Macromolecule #7: 60S ribosomal protein L13a
+Macromolecule #8: 60S ribosomal protein L14
+Macromolecule #9: 60S ribosomal protein L15
+Macromolecule #10: 60S ribosomal protein L17
+Macromolecule #11: 60S ribosomal protein L18
+Macromolecule #12: 60S ribosomal protein L18a
+Macromolecule #13: 60S ribosomal protein L19
+Macromolecule #14: 60S ribosomal protein L21
+Macromolecule #15: 60S ribosomal protein L22
+Macromolecule #16: 60S ribosomal protein L23
+Macromolecule #17: 60S ribosomal protein L23a
+Macromolecule #18: 60S ribosomal protein L26
+Macromolecule #19: 60S ribosomal protein L27
+Macromolecule #20: 60S ribosomal protein L27a
+Macromolecule #21: 60S ribosomal protein L28
+Macromolecule #22: 60S ribosomal protein L29
+Macromolecule #23: 60S ribosomal protein L3
+Macromolecule #24: 60S ribosomal protein L30
+Macromolecule #25: 60S ribosomal protein L31
+Macromolecule #26: 60S ribosomal protein L32
+Macromolecule #27: 60S ribosomal protein L34
+Macromolecule #28: 60S ribosomal protein L35
+Macromolecule #29: 60S ribosomal protein L35a
+Macromolecule #30: 60S ribosomal protein L36
+Macromolecule #31: 60S ribosomal protein L36a
+Macromolecule #32: 60S ribosomal protein L37
+Macromolecule #33: 60S ribosomal protein L37a
+Macromolecule #34: 60S ribosomal protein L38
+Macromolecule #35: 60S ribosomal protein L39
+Macromolecule #36: Protein LLP homolog
+Macromolecule #37: Zinc finger protein 593
+Macromolecule #38: Translation machinery-associated protein 16
+Macromolecule #39: 60S ribosomal protein L4
+Macromolecule #40: 60S ribosomal protein L5
+Macromolecule #41: 60S ribosomal protein L6
+Macromolecule #42: 60S ribosomal protein L7
+Macromolecule #43: 60S ribosomal protein L7a
+Macromolecule #44: 60S ribosomal protein L8
+Macromolecule #45: 60S ribosomal protein L9
+Macromolecule #46: Eukaryotic translation initiation factor 6
+Macromolecule #47: mRNA turnover protein 4 homolog
+Macromolecule #48: GTP-binding protein 4
+Macromolecule #49: Probable ribosome biogenesis protein RLP24
+Macromolecule #50: Leydig cell tumor 10 kDa protein homolog
+Macromolecule #2: 5.8S rRNA
+Macromolecule #3: 28S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #51: MAGNESIUM ION
+Macromolecule #52: ZINC ION
+Macromolecule #53: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #54: POTASSIUM 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-8flc: |