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Open data
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Basic information
Entry | Database: PDB / ID: 8fkt | |||||||||
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Title | Human nucleolar pre-60S ribosomal subunit (State C1) | |||||||||
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![]() | RIBOSOME / Pre-60S ribosomal subunit / Assembly intermediate / Nucleoprotein complex | |||||||||
Function / homology | ![]() RNA 2'-O-methyltransferase activity / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / positive regulation of protein localization to chromosome, telomeric region / RNA metabolic process / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity ...RNA 2'-O-methyltransferase activity / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / positive regulation of protein localization to chromosome, telomeric region / RNA metabolic process / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / RNA methylation / regulation of megakaryocyte differentiation / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / stem cell division / PeBoW complex / miRNA-mediated gene silencing by inhibition of translation / positive regulation of telomere maintenance / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / rRNA base methylation / rRNA primary transcript binding / 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 / rRNA methylation / regulation of reactive oxygen species metabolic process / rRNA modification in the nucleus and cytosol / regulation of glycolytic process / A band / 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 / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of ubiquitin protein ligase activity / preribosome, small subunit precursor / mitotic metaphase chromosome alignment / stem cell population maintenance / regulation of cyclin-dependent protein serine/threonine kinase activity / rRNA metabolic process / G1 to G0 transition / negative regulation of cell-cell adhesion / homeostatic process / positive regulation of dendritic spine development / maturation of 5.8S rRNA / negative regulation of DNA replication / macrophage chemotaxis / lung morphogenesis / Protein hydroxylation / ribosomal large subunit binding / 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 / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / estrogen receptor signaling pathway / cellular response to interleukin-4 / hematopoietic progenitor cell differentiation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal subunit export from nucleus / cellular response to actinomycin D / RNA processing / ribonucleoprotein complex binding / cytosolic ribosome / 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 / 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 / maturation of LSU-rRNA / Transferases; Transferring one-carbon groups; Methyltransferases / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / ribosome assembly / 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 / condensed nuclear chromosome Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 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 | ![]() | 3.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 29256MC ![]() 8fkpC ![]() 8fkqC ![]() 8fkrC ![]() 8fksC ![]() 8fkuC ![]() 8fkvC ![]() 8fkwC ![]() 8fkxC ![]() 8fkyC ![]() 8fkzC ![]() 8fl0C ![]() 8fl2C ![]() 8fl3C ![]() 8fl4C ![]() 8fl6C ![]() 8fl7C ![]() 8fl9C ![]() 8flaC ![]() 8flbC ![]() 8flcC ![]() 8fldC ![]() 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 ... , 26 types, 26 molecules BABBL6L7L8L9LALBLCLELGLHLILKLNLQLSLTLULWSASCSDSESGSI
-RNA chain , 3 types, 3 molecules L1L2L3
#3: RNA chain | Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#4: RNA chain | Mass: 376425.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: RNA chain | Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 19 types, 19 molecules NBNHNKNMNONQNSSHSJSKSLSMSNSQSRSTSVSYSZ
#24: Protein | Mass: 62098.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#26: Protein | Mass: 20491.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#28: Protein | Mass: 15268.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#29: Protein | Mass: 35469.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#30: Protein | Mass: 52927.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#31: Protein | Mass: 42501.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#32: Protein | Mass: 40189.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#38: Protein | Mass: 34285.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#40: Protein | Mass: 96726.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q8IY81, Transferases; Transferring one-carbon groups; Methyltransferases |
#41: Protein | Mass: 26620.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#42: Protein | Mass: 55089.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#43: Protein | Mass: 68114.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#44: Protein | Mass: 34925.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#46: Protein | Mass: 27602.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#47: Protein | Mass: 74107.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#49: Protein | Mass: 41278.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#50: Protein | Mass: 19666.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#52: Protein | Mass: 89441.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P46087, Transferases; Transferring one-carbon groups; Methyltransferases |
#53: Protein | Mass: 21234.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Ribosome biogenesis protein ... , 3 types, 3 molecules NFSOSS
#25: Protein | Mass: 30136.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#45: Protein | Mass: 41483.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#48: Protein | Mass: 83901.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-ATP-dependent RNA helicase ... , 2 types, 2 molecules NISW
#27: Protein | Mass: 98769.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#51: Protein | Mass: 75526.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 6 types, 70 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/K.gif)
#54: Chemical | ChemComp-MG / #55: Chemical | #56: Chemical | ChemComp-ADP / | #57: Chemical | ChemComp-SF4 / | #58: Chemical | ChemComp-GDP / | #59: Chemical | ChemComp-K / | |
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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 nucleolar pre-60S ribosomal subunit (State C1) / Type: RIBOSOME / Entity ID: #1-#53 / 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: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45396 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL |