+Open data
-Basic information
Entry | Database: PDB / ID: 8fl4 | |||||||||
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Title | Human nuclear pre-60S ribosomal subunit (State I3) | |||||||||
Components |
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Keywords | RIBOSOME / Pre-60S ribosomal subunit / Assembly intermediate / Nucleoprotein complex | |||||||||
Function / homology | Function and homology information : / Las1 complex / protein localization to nucleoplasm / inner cell mass cell differentiation / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to chromosome, telomeric region / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding ...: / Las1 complex / protein localization to nucleoplasm / inner cell mass cell differentiation / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to chromosome, telomeric region / regulation of RIG-I signaling pathway / 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 / dynein axonemal particle / PTK6 Expression / regulation of megakaryocyte differentiation / PeBoW complex / SUMO binding / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / stem cell division / negative regulation of signal transduction by p53 class mediator / eukaryotic 80S initiation complex / negative regulation of protein neddylation / miRNA-mediated gene silencing by inhibition of translation / nuclear pre-replicative complex / translation at presynapse / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / positive regulation of telomere maintenance / ribosomal protein import into nucleus / 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 / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of protein K63-linked deubiquitination / blastocyst formation / TORC2 complex binding / protein localization to nucleolus / GAIT complex / G1 to G0 transition / middle ear morphogenesis / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / skeletal system morphogenesis / cytoplasmic side of rough endoplasmic reticulum membrane / A band / nuclear-transcribed mRNA catabolic process / regulation of reactive oxygen species metabolic process / positive regulation of signal transduction by p53 class mediator / alpha-beta T cell differentiation / ubiquitin ligase inhibitor activity / regulation of glycolytic process / negative regulation of ubiquitin protein ligase activity / regulation of aerobic respiration / response to aldosterone / maturation of 5.8S rRNA / homeostatic process / stem cell population maintenance / positive regulation of dendritic spine development / lung morphogenesis / macrophage chemotaxis / negative regulation of DNA replication / negative regulation of cell-cell adhesion / ribosomal subunit export from nucleus / Protein hydroxylation / regulation of cyclin-dependent protein serine/threonine kinase activity / Peptide chain elongation / ribosomal large subunit binding / mitotic G2 DNA damage checkpoint signaling / Selenocysteine synthesis / protein-RNA complex assembly / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / blastocyst development / preribosome, large subunit precursor / Response of EIF2AK4 (GCN2) to amino acid deficiency / MLL1 complex / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / cellular response to actinomycin D / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / negative regulation of mitotic cell cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit export from nucleus / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / protein targeting / rough endoplasmic reticulum / Major pathway of rRNA processing in the nucleolus and cytosol / MDM2/MDM4 family protein binding / cellular response to estrogen stimulus / negative regulation of protein-containing complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / somitogenesis Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | |||||||||
Authors | Vanden Broeck, A. / Klinge, S. | |||||||||
Funding support | European Union, United States, 2items
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Citation | Journal: Science / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fl4.cif.gz | 4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8fl4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fl4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/8fl4 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/8fl4 | HTTPS FTP |
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-Related structure data
Related structure data | 29267MC 8fkpC 8fkqC 8fkrC 8fksC 8fktC 8fkuC 8fkvC 8fkwC 8fkxC 8fkyC 8fkzC 8fl0C 8fl2C 8fl3C 8fl6C 8fl7C 8fl9C 8flaC 8flbC 8flcC 8fldC 8fleC 8flfC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+60S ribosomal protein ... , 39 types, 39 molecules BABBL5L6L7L8L9LALBLCLDLELFLGLHLILJLKLLLNLOLPLQLRLSLTLULWLXLY...
-Protein , 16 types, 18 molecules BDNBNCNJNKNPNTNUNVNWNXNYNZSKSMSQSRSV
#3: Protein | Mass: 83153.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9Y4W2 | ||||||||||||||
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#36: Protein | Mass: 62098.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BVP2 | ||||||||||||||
#37: Protein | Mass: 83796.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q13823 | ||||||||||||||
#39: Protein | Mass: 53387.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9NVX2 | ||||||||||||||
#40: Protein | Mass: 15268.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BRT6 | ||||||||||||||
#42: Protein | Mass: 15230.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O00488 | ||||||||||||||
#43: Protein | Mass: 80005.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9NVU7 | ||||||||||||||
#44: Protein | Mass: 105811.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9NXF1 | ||||||||||||||
#45: Protein | Mass: 47459.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BV38 #46: Protein | Mass: 119786.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q8IZL8 #47: Protein | | Mass: 40312.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9H6F5 #56: Protein | | Mass: 26620.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P56537 #57: Protein | | Mass: 68114.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O00541 #58: Protein | | Mass: 27602.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9UKD2 #59: Protein | | Mass: 74107.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BZE4 #60: Protein | | Mass: 19666.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9UHA3 |
-RNA chain , 3 types, 3 molecules L1L3L4
#4: RNA chain | Mass: 50463.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 555853 |
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#5: RNA chain | Mass: 1641203.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 86475748 |
#6: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 23898 |
-Ribosome biogenesis protein ... , 2 types, 2 molecules NFNL
#38: Protein | Mass: 30136.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O95478 |
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#41: Protein | Mass: 54498.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9NZM5 |
-Non-polymers , 5 types, 108 molecules
#61: Chemical | ChemComp-MG / #62: Chemical | ChemComp-ZN / #63: Chemical | ChemComp-GTP / | #64: Chemical | #65: Chemical | ChemComp-GDP / | |
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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 |
-Sample preparation
Component | Name: Human nuclear pre-60S ribosomal subunit (State I3) / Type: RIBOSOME / Entity ID: #1-#60 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) / Strain: HEK293F |
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. |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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 |
-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: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22406 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL |