+Open data
-Basic information
Entry | Database: PDB / ID: 7ozs | ||||||||||||
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Title | Structure of the hexameric 5S RNP from C. thermophilum | ||||||||||||
Components |
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Keywords | RNA BINDING PROTEIN / 5S RNP / Ribosome biogenesis / Symportin 1 / Rpf2-Rrs1 | ||||||||||||
Function / homology | Function and homology information preribosome, large subunit precursor / 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) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / protein import into nucleus / unfolded protein binding / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome ...preribosome, large subunit precursor / 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) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / protein import into nucleus / unfolded protein binding / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / nucleolus / RNA binding Similarity search - Function | ||||||||||||
Biological species | Thermochaetoides thermophila DSM 1495 (fungus) Chaetomium thermophilum (fungus) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||
Authors | Castillo, N. / Thoms, M. / Flemming, D. / Hammaren, H.M. / Buschauer, R. / Ameismeier, M. / Bassler, J. / Beck, M. / Beckmann, R. / Hurt, E. | ||||||||||||
Funding support | Germany, 3items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structure of nascent 5S RNPs at the crossroad between ribosome assembly and MDM2-p53 pathways. Authors: Nestor Miguel Castillo Duque de Estrada / Matthias Thoms / Dirk Flemming / Henrik M Hammaren / Robert Buschauer / Michael Ameismeier / Jochen Baßler / Martin Beck / Roland Beckmann / Ed Hurt / Abstract: The 5S ribonucleoprotein (RNP) is assembled from its three components (5S rRNA, Rpl5/uL18 and Rpl11/uL5) before being incorporated into the pre-60S subunit. However, when ribosome synthesis is ...The 5S ribonucleoprotein (RNP) is assembled from its three components (5S rRNA, Rpl5/uL18 and Rpl11/uL5) before being incorporated into the pre-60S subunit. However, when ribosome synthesis is disturbed, a free 5S RNP can enter the MDM2-p53 pathway to regulate cell cycle and apoptotic signaling. Here we reconstitute and determine the cryo-electron microscopy structure of the conserved hexameric 5S RNP with fungal or human factors. This reveals how the nascent 5S rRNA associates with the initial nuclear import complex Syo1-uL18-uL5 and, upon further recruitment of the nucleolar factors Rpf2 and Rrs1, develops into the 5S RNP precursor that can assemble into the pre-ribosome. In addition, we elucidate the structure of another 5S RNP intermediate, carrying the human ubiquitin ligase Mdm2, which unravels how this enzyme can be sequestered from its target substrate p53. Our data provide molecular insight into how the 5S RNP can mediate between ribosome biogenesis and cell proliferation. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ozs.cif.gz | 304.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ozs.ent.gz | 232.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ozs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ozs_validation.pdf.gz | 770.1 KB | Display | wwPDB validaton report |
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Full document | 7ozs_full_validation.pdf.gz | 777.5 KB | Display | |
Data in XML | 7ozs_validation.xml.gz | 43.8 KB | Display | |
Data in CIF | 7ozs_validation.cif.gz | 70 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/7ozs ftp://data.pdbj.org/pub/pdb/validation_reports/oz/7ozs | HTTPS FTP |
-Related structure data
Related structure data | 13134MC 8bguC M: map data used to model this data C: citing same article (ref.) |
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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
-Protein , 5 types, 5 molecules BADCF
#1: Protein | Mass: 20119.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SHQ2 |
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#2: Protein | Mass: 35034.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SEG2 |
#3: Protein | Mass: 22817.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SCH6 |
#4: Protein | Mass: 39927.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0SF80 |
#7: Protein | Mass: 74709.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / References: UniProt: G0S5S6 |
-RNA chain / Protein/peptide , 2 types, 2 molecules 3E
#5: RNA chain | Mass: 38312.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
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#6: Protein/peptide | Mass: 1975.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) |
-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: hexameric 5S RNP from C. thermophilum / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 43.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126547 / Symmetry type: POINT |