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Open data
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Basic information
Entry | Database: PDB / ID: 8fld | |||||||||
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Title | Human nuclear pre-60S ribosomal subunit (State L1) | |||||||||
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![]() | RIBOSOME / Pre-60S ribosomal subunit / Assembly intermediate / 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 / embryonic brain development / eukaryotic 80S initiation complex / 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 / blastocyst formation / positive regulation of protein K63-linked deubiquitination / protein localization to nucleolus / TORC2 complex binding / GAIT complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / middle ear morphogenesis / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of reactive oxygen species metabolic process / regulation of glycolytic process / A band / alpha-beta T cell differentiation / regulation of G1 to G0 transition / nuclear-transcribed mRNA catabolic 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 / negative regulation of ubiquitin protein ligase activity / regulation of aerobic respiration / response to aldosterone / regulation of cyclin-dependent protein serine/threonine kinase activity / G1 to G0 transition / rRNA metabolic process / positive regulation of dendritic spine development / homeostatic process / negative regulation of cell-cell adhesion / negative regulation of DNA replication / maturation of 5.8S rRNA / lung morphogenesis / Protein hydroxylation / macrophage chemotaxis / Peptide chain elongation / mitotic G2 DNA damage checkpoint signaling / ribosomal large subunit binding / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / rRNA transcription / blastocyst development / preribosome, large subunit precursor / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein-RNA complex assembly / 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) / translation regulator activity / cellular response to actinomycin D / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / cytosolic ribosome / 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 / ossification / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / assembly of large subunit precursor of preribosome / regulation of signal transduction by p53 class mediator Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 274.6 KB | Display | |
Data in CIF | ![]() | 456 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 29275MC ![]() 8fkpC ![]() 8fkqC ![]() 8fkrC ![]() 8fksC ![]() 8fktC ![]() 8fkuC ![]() 8fkvC ![]() 8fkwC ![]() 8fkxC ![]() 8fkyC ![]() 8fkzC ![]() 8fl0C ![]() 8fl2C ![]() 8fl3C ![]() 8fl4C ![]() 8fl6C ![]() 8fl7C ![]() 8fl9C ![]() 8flaC ![]() 8flbC ![]() 8flcC ![]() 8fleC ![]() 8flfC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
+60S ribosomal protein ... , 40 types, 40 molecules BEL5L6L7L8L9LALBLCLDLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLX...
-RNA chain , 4 types, 4 molecules L1L2L3L4
#2: RNA chain | Mass: 50463.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#3: RNA chain | Mass: 376425.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: RNA chain | Mass: 1641203.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 10 types, 10 molecules NKNLNPSHSKSLSMSQSRSV
#37: Protein | Mass: 15268.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#38: Protein | Mass: 54498.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#39: Protein | Mass: 15230.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#47: Protein | Mass: 34285.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#49: Protein | Mass: 26620.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#50: Protein | Mass: 55089.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#51: Protein | Mass: 68114.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#52: Protein | Mass: 27602.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#53: Protein | Mass: 74107.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#54: Protein | Mass: 19666.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 2 types, 93 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#55: Chemical | ChemComp-MG / #56: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human nuclear pre-60S ribosomal subunit (State L1) / Type: RIBOSOME / Entity ID: #1-#54 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R3.5/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K Details: Four applications with manual blotting before last blotting with the Vitrobot. |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Average exposure time: 2 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 172699 |
EM imaging optics | Energyfilter slit width: 20 eV |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 15679142 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88174 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL |