+Open data
-Basic information
Entry | Database: PDB / ID: 8fkw | |||||||||
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Title | Human nucleolar pre-60S ribosomal subunit (State D2) | |||||||||
Components |
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Keywords | RIBOSOME / Pre-60S ribosomal subunit / Assembly intermediate / Nucleoprotein complex | |||||||||
Function / homology | Function and homology information RNA 2'-O-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / RNA metabolic process / negative regulation of collagen binding / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity ...RNA 2'-O-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / RNA metabolic process / negative regulation of collagen binding / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / PeBoW complex / RNA methylation / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / stem cell division / miRNA-mediated gene silencing by inhibition of translation / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / positive regulation of telomere maintenance / rRNA base methylation / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / blastocyst formation / TORC2 complex binding / protein localization to nucleolus / GAIT complex / G1 to G0 transition / negative regulation of B cell apoptotic process / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / rRNA modification in the nucleus and cytosol / A band / nuclear-transcribed mRNA catabolic process / regulation of reactive oxygen species metabolic process / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / regulation of glycolytic process / negative regulation of ubiquitin protein ligase activity / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / mitotic metaphase chromosome alignment / rRNA metabolic process / 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 / fat cell differentiation / ribosomal subunit export from nucleus / Protein hydroxylation / 90S preribosome / regulation of cyclin-dependent protein serine/threonine kinase activity / Peptide chain elongation / ribosomal large subunit binding / Selenocysteine synthesis / rRNA transcription / 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 / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / cellular response to actinomycin D / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / DNA replication initiation / nucleosome binding / L13a-mediated translational silencing of Ceruloplasmin expression / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / MDM2/MDM4 family protein binding / intracellular estrogen receptor signaling pathway / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / hematopoietic progenitor cell differentiation / negative regulation of intrinsic apoptotic signaling pathway / RNA processing / ribonucleoprotein complex binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal large subunit biogenesis / maturation of LSU-rRNA / negative regulation of protein ubiquitination / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 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 | 8fkw.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8fkw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fk/8fkw ftp://data.pdbj.org/pub/pdb/validation_reports/fk/8fkw | HTTPS FTP |
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-Related structure data
Related structure data | 29259MC 8fkpC 8fkqC 8fkrC 8fksC 8fktC 8fkuC 8fkvC 8fkxC 8fkyC 8fkzC 8fl0C 8fl2C 8fl3C 8fl4C 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 ... , 28 types, 28 molecules BABBL6L7L8L9LALBLCLELGLHLILKLLLNLPLQLSLTLULWSASCSDSESGSI
-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) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 555853 |
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#4: RNA chain | Mass: 376425.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 86475748 |
#5: RNA chain | Mass: 1640222.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: GenBank: 86475748 |
-Nucleolar complex protein ... , 2 types, 2 molecules NASU
#26: Protein | Mass: 85028.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9Y3T9 |
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#49: Protein | Mass: 92709.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q8WTT2 |
-Protein , 15 types, 15 molecules NBNHNKSHSJSKSLSMSNSQSRSTSVSYSZ
#27: 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 |
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#29: Protein | Mass: 20491.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9Y221 |
#31: 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 |
#37: Protein | Mass: 34285.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9BYG3 |
#39: Protein | Mass: 96726.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F References: UniProt: Q8IY81, Transferases; Transferring one-carbon groups; Methyltransferases |
#40: 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 |
#41: Protein | Mass: 55089.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: O76021 |
#42: 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 |
#43: Protein | Mass: 34925.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q99848 |
#45: 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 |
#46: 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 |
#48: Protein | Mass: 41278.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q15050 |
#50: 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 |
#52: Protein | Mass: 89441.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F 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) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9Y3C1 |
-Ribosome biogenesis protein ... , 3 types, 3 molecules NFSOSS
#28: 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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#44: Protein | Mass: 41483.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q8TDN6 |
#47: Protein | Mass: 83901.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q14137 |
-ATP-dependent RNA helicase ... , 2 types, 2 molecules NISW
#30: Protein | Mass: 98769.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q8TDD1, RNA helicase |
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#51: Protein | Mass: 75526.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: Q9NVP1, RNA helicase |
-Non-polymers , 5 types, 64 molecules
#54: Chemical | ChemComp-MG / #55: Chemical | #56: Chemical | ChemComp-ADP / | #57: Chemical | ChemComp-GDP / | #58: 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 |
-Sample preparation
Component | Name: Human nucleolar pre-60S ribosomal subunit (State D2) / Type: RIBOSOME / Entity ID: #1-#53 / 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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 214795 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL |