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Open data
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Basic information
Entry | Database: PDB / ID: 6wnv | |||||||||||||||
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Title | 70S ribosome without free 5S rRNA and with a perturbed PTC | |||||||||||||||
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Function / homology | ![]() negative regulation of cytoplasmic translational initiation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Loveland, A.B. / Korostelev, A.A. / Mankin, A.S. / Huang, S. / Aleksashin, N.A. / Klepacki, D. / Reier, K. / Kefi, A. / Szal, A. / Remme, J. ...Loveland, A.B. / Korostelev, A.A. / Mankin, A.S. / Huang, S. / Aleksashin, N.A. / Klepacki, D. / Reier, K. / Kefi, A. / Szal, A. / Remme, J. / Jaeger, L. / Vazquez-Laslop, N. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Ribosome engineering reveals the importance of 5S rRNA autonomy for ribosome assembly. Authors: Shijie Huang / Nikolay A Aleksashin / Anna B Loveland / Dorota Klepacki / Kaspar Reier / Amira Kefi / Teresa Szal / Jaanus Remme / Luc Jaeger / Nora Vázquez-Laslop / Andrei A Korostelev / Alexander S Mankin / ![]() ![]() Abstract: 5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. ...5S rRNA is an indispensable component of cytoplasmic ribosomes in all species. The functions of 5S rRNA and the reasons for its evolutionary preservation as an independent molecule remain unclear. Here we used ribosome engineering to investigate whether 5S rRNA autonomy is critical for ribosome function and cell survival. By linking circularly permutated 5S rRNA with 23S rRNA we generated a bacterial strain devoid of free 5S rRNA. Viability of the engineered cells demonstrates that autonomous 5S rRNA is dispensable for cell growth under standard conditions and is unlikely to have essential functions outside the ribosome. The fully assembled ribosomes carrying 23S-5S rRNA are highly active in translation. However, the engineered cells accumulate aberrant 50S subunits unable to form stable 70S ribosomes. Cryo-EM analysis revealed a malformed peptidyl transferase center in the misassembled 50S subunits. Our results argue that the autonomy of 5S rRNA is preserved due to its role in ribosome biogenesis. | |||||||||||||||
History |
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Structure visualization
Movie |
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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 | ![]() 21857MC ![]() 6wntC ![]() 6wnwC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
+50S ribosomal protein ... , 30 types, 30 molecules bcdefghijklnopqrstuvwxyzABDEFa
-30S ribosomal protein ... , 20 types, 20 molecules GHIJKLMNOPQRSTUVWXYZ
#30: Protein | ![]() Mass: 25015.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
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#31: Protein | ![]() Mass: 23078.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#32: Protein | ![]() Mass: 23383.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#33: Protein | ![]() Mass: 16532.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#34: Protein | ![]() Mass: 11669.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#35: Protein | ![]() Mass: 16861.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#36: Protein | ![]() Mass: 14015.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#37: Protein | ![]() Mass: 14554.882 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#38: Protein | ![]() Mass: 11196.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#39: Protein | ![]() Mass: 12388.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#40: Protein | ![]() Mass: 13636.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#41: Protein | ![]() Mass: 12625.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#42: Protein | ![]() Mass: 11475.364 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#43: Protein | ![]() Mass: 10159.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#44: Protein | ![]() Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#45: Protein | ![]() Mass: 9263.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#46: Protein | ![]() Mass: 7606.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#47: Protein | ![]() Mass: 9057.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#48: Protein | ![]() Mass: 9506.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
#49: Protein | ![]() Mass: 7763.073 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
-RNA chain , 2 types, 2 molecules 34
#51: RNA chain | ![]() Mass: 498725.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() ![]() ![]() |
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#52: RNA chain | Mass: 982729.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Engineered 23S rRNA with inserted circularly permuted 5S rRNA Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: 70S ribosome without free 5S rRNA and with perturbed PTC Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 2.5 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: TFS TALOS |
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Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction![]() | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 489732 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9620 / Symmetry type: POINT | ||||||||||||||||||||||||||||
NMR ensemble | Conformers submitted total number: 1 |