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- EMDB-29272: Human nuclear pre-60S ribosomal subunit (State K1) - 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 K1) - Composite map | |||||||||
![]() | Human nuclear pre-60S ribosomal subunit (State K1) | |||||||||
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![]() | Pre-60S ribosomal subunit / Assembly intermediate / Ribosome / Nucleoprotein complex | |||||||||
Function / homology | ![]() protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament ...protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / negative regulation of signal transduction by p53 class mediator / PeBoW complex / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / positive regulation of protein K63-linked deubiquitination / blastocyst formation / protein localization to nucleolus / TORC2 complex binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GAIT complex / middle ear morphogenesis / regulation of reactive oxygen species metabolic process / regulation of glycolytic process / A band / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation / regulation of G1 to G0 transition / 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 / negative regulation of ubiquitin protein ligase activity / regulation of aerobic respiration / response to aldosterone / regulation of cyclin-dependent protein serine/threonine kinase activity / rRNA metabolic process / negative regulation of cell-cell adhesion / G1 to G0 transition / positive regulation of dendritic spine development / homeostatic process / maturation of 5.8S rRNA / negative regulation of DNA replication / macrophage chemotaxis / lung morphogenesis / Protein hydroxylation / ribosomal large subunit binding / mitotic G2 DNA damage checkpoint signaling / Peptide chain elongation / Selenocysteine synthesis / rRNA transcription / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / nuclear-transcribed mRNA catabolic process / Eukaryotic Translation Termination / blastocyst development / preribosome, large subunit precursor / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein localization to nucleus / condensed nuclear chromosome / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / protein-RNA complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / cellular response to interleukin-4 / negative regulation of protein-containing complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal subunit export from nucleus / negative regulation of ubiquitin-dependent protein catabolic process / ossification / cellular response to actinomycin D / ribonucleoprotein complex binding / cytosolic ribosome / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of cell migration / innate immune response in mucosa Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.63 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 | ![]() | 125.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 81.9 KB 81.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.8 KB | Display | ![]() |
Images | ![]() | 153.3 KB | ||
Masks | ![]() | 421.9 MB | ![]() | |
Others | ![]() ![]() | 391.1 MB 391.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8flaMC ![]() 8fkpC ![]() 8fkqC ![]() 8fkrC ![]() 8fksC ![]() 8fktC ![]() 8fkuC ![]() 8fkvC ![]() 8fkwC ![]() 8fkxC ![]() 8fkyC ![]() 8fkzC ![]() 8fl0C ![]() 8fl2C ![]() 8fl3C ![]() 8fl4C ![]() 8fl6C ![]() 8fl7C ![]() 8fl9C ![]() 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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Annotation | Human nuclear pre-60S ribosomal subunit (State K1) | ||||||||||||||||||||
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_29272_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_29272_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 K1)
+Supramolecule #1: Human nuclear pre-60S ribosomal subunit (State K1)
+Macromolecule #1: 60S ribosomal protein L12
+Macromolecule #6: 60S ribosomal protein L11
+Macromolecule #7: 60S ribosomal protein L13
+Macromolecule #8: 60S ribosomal protein L13a
+Macromolecule #9: 60S ribosomal protein L14
+Macromolecule #10: 60S ribosomal protein L15
+Macromolecule #11: 60S ribosomal protein L17
+Macromolecule #12: 60S ribosomal protein L18
+Macromolecule #13: 60S ribosomal protein L18a
+Macromolecule #14: 60S ribosomal protein L19
+Macromolecule #15: 60S ribosomal protein L21
+Macromolecule #16: 60S ribosomal protein L22
+Macromolecule #17: 60S ribosomal protein L23
+Macromolecule #18: 60S ribosomal protein L23a
+Macromolecule #19: 60S ribosomal protein L26
+Macromolecule #20: 60S ribosomal protein L27
+Macromolecule #21: 60S ribosomal protein L27a
+Macromolecule #22: 60S ribosomal protein L28
+Macromolecule #23: 60S ribosomal protein L29
+Macromolecule #24: 60S ribosomal protein L3
+Macromolecule #25: 60S ribosomal protein L30
+Macromolecule #26: 60S ribosomal protein L31
+Macromolecule #27: 60S ribosomal protein L32
+Macromolecule #28: 60S ribosomal protein L34
+Macromolecule #29: 60S ribosomal protein L35
+Macromolecule #30: 60S ribosomal protein L35a
+Macromolecule #31: 60S ribosomal protein L36
+Macromolecule #32: 60S ribosomal protein L36a
+Macromolecule #33: 60S ribosomal protein L37
+Macromolecule #34: 60S ribosomal protein L37a
+Macromolecule #35: 60S ribosomal protein L38
+Macromolecule #36: 60S ribosomal protein L39
+Macromolecule #37: Protein LLP homolog
+Macromolecule #38: Ribosome biogenesis protein NOP53
+Macromolecule #39: Zinc finger protein 593
+Macromolecule #40: Translation machinery-associated protein 16
+Macromolecule #41: 60S ribosomal protein L4
+Macromolecule #42: 60S ribosomal protein L5
+Macromolecule #43: 60S ribosomal protein L6
+Macromolecule #44: 60S ribosomal protein L7
+Macromolecule #45: 60S ribosomal protein L7a
+Macromolecule #46: 60S ribosomal protein L8
+Macromolecule #47: 60S ribosomal protein L9
+Macromolecule #48: MKI67 FHA domain-interacting nucleolar phosphoprotein
+Macromolecule #49: 60S ribosomal protein L7-like 1
+Macromolecule #50: Eukaryotic translation initiation factor 6
+Macromolecule #51: Ribosomal L1 domain-containing protein 1
+Macromolecule #52: Pescadillo homolog
+Macromolecule #53: mRNA turnover protein 4 homolog
+Macromolecule #54: GTP-binding protein 4
+Macromolecule #55: Probable ribosome biogenesis protein RLP24
+Macromolecule #56: Leydig cell tumor 10 kDa protein homolog
+Macromolecule #2: 5.8S rRNA
+Macromolecule #3: ITS2 rRNA
+Macromolecule #4: 28S rRNA
+Macromolecule #5: 5S rRNA
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: ZINC ION
+Macromolecule #59: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #60: 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-8fla: |