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- PDB-8v9l: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8v9l | ||||||||||||
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Title | Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Composite structure 6) | ||||||||||||
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![]() | RIBOSOME / cryo-EM / mycobacteria / hibernation / Msmeg1130 / Balon / MsmegEF-Tu | ||||||||||||
Function / homology | ![]() translation elongation factor activity / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit ...translation elongation factor activity / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||||||||
![]() | Rybak, M.Y. / Helena-Bueno, K. / Hill, C.H. / Melnikov, S.V. / Gagnon, M.G. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: A new family of bacterial ribosome hibernation factors. Authors: Karla Helena-Bueno / Mariia Yu Rybak / Chinenye L Ekemezie / Rudi Sullivan / Charlotte R Brown / Charlotte Dingwall / Arnaud Baslé / Claudia Schneider / James P R Connolly / James N Blaza / ...Authors: Karla Helena-Bueno / Mariia Yu Rybak / Chinenye L Ekemezie / Rudi Sullivan / Charlotte R Brown / Charlotte Dingwall / Arnaud Baslé / Claudia Schneider / James P R Connolly / James N Blaza / Bálint Csörgő / Patrick J Moynihan / Matthieu G Gagnon / Chris H Hill / Sergey V Melnikov / ![]() ![]() ![]() Abstract: To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of ...To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 3.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
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-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 223.3 KB | Display | |
Data in CIF | ![]() | 397.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 43076MC ![]() 8rd8C ![]() 8rdvC ![]() 8rdwC ![]() 8v9jC ![]() 8v9kC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 5 types, 5 molecules avyAB
#1: RNA chain | Mass: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: GenBank: 118168627 |
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#22: RNA chain | Mass: 1179.706 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 |
#24: RNA chain | Mass: 24531.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 |
#26: RNA chain | Mass: 1026283.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: GenBank: 118168627 |
#27: RNA chain | Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: GenBank: 118168627 |
-30S Ribosomal Protein ... , 15 types, 15 molecules bcdfgijklmpqstu
#2: Protein | Mass: 30145.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QVB8 |
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#3: Protein | Mass: 30191.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSD7 |
#4: Protein | Mass: 23415.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSL7 |
#6: Protein | Mass: 10991.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0A2U9Q0X2 |
#7: Protein | Mass: 17660.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QS97 |
#9: Protein | Mass: 16794.365 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSP9 |
#10: Protein | Mass: 11454.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSD0 |
#11: Protein | Mass: 14671.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSL6 |
#12: Protein | Mass: 13896.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QS96 |
#13: Protein | Mass: 14249.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSL5 |
#16: Protein | Mass: 16795.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QV37 |
#17: Protein | Mass: 11127.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSE0 |
#19: Protein | Mass: 10800.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSD5 |
#20: Protein | Mass: 9556.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0R102 |
#21: Protein/peptide | Mass: 4164.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 |
-Small ribosomal subunit protein ... , 5 types, 5 molecules ehnor
#5: Protein | Mass: 21946.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSG6 |
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#8: Protein | Mass: 14492.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSG3 |
#14: Protein | Mass: 6976.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSG2 |
#15: Protein | Mass: 10368.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QVQ3 |
#18: Protein | Mass: 9524.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0R7F7 |
-Protein , 2 types, 2 molecules xz
#23: Protein | Mass: 43792.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MsmegEF-Tu Source: (gene. exp.) ![]() Strain: MC2155 / Gene: tuf / Plasmid: pET28-SMT3-MsmegEF-Tu / Production host: ![]() ![]() |
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#25: Protein | Mass: 41390.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MSMEG_1130 Source: (gene. exp.) ![]() Strain: MC2155 / Gene: MSMEG_1130 / Plasmid: pET28-SMT3-MSMEG_1130 / Production host: ![]() ![]() |
-50S ribosomal protein ... , 20 types, 20 molecules CDGHIJMNPRWXY1246789
#28: Protein | Mass: 30425.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSD4 |
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#29: Protein | Mass: 23011.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSD1 |
#32: Protein | Mass: 19483.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSG4 |
#33: Protein | Mass: 15949.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0R7F6 |
#34: Protein | Mass: 18035.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QS62 |
#35: Protein | Mass: 15023.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QS45 |
#37: Protein | Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSF9 |
#38: Protein | Mass: 15602.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSG8 |
#40: Protein | Mass: 21892.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSL9 |
#42: Protein | Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QV42 |
#47: Protein | Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSG0 |
#48: Protein | Mass: 22571.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0R3D2 |
#49: Protein | Mass: 9249.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0R150 |
#51: Protein | Mass: 8790.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSD9 |
#52: Protein | Mass: 7022.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSG7 |
#54: Protein | Mass: 6467.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0R3I9 |
#56: Protein/peptide | Mass: 5522.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0R7K0 |
#57: Protein | Mass: 7298.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QYU7 |
#58: Protein/peptide | Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSL4 |
#59: Protein/peptide | Mass: 2841.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QTP4 |
-Large ribosomal subunit protein ... , 12 types, 12 molecules EFLOQSTUVZ35
#30: Protein | Mass: 22920.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSD2 |
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#31: Protein | Mass: 21152.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSG1 |
#36: Protein | Mass: 16146.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSP8 |
#39: Protein | Mass: 15627.065 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSD8 |
#41: Protein | Mass: 13711.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: I7FGD9 |
#43: Protein | Mass: 14494.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QYU6 |
#44: Protein | Mass: 11055.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0R151 |
#45: Protein | Mass: 16353.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSD6 |
#46: Protein | Mass: 11047.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QSD3 |
#50: Protein | Mass: 6891.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: I7FJ52 |
#53: Protein | Mass: 8312.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0R215 |
#55: Protein | Mass: 6468.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: MC2155 / References: UniProt: A0QS39 |
-Non-polymers , 2 types, 3 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#60: Chemical | ChemComp-GDP / |
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#61: Chemical |
-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: Cryo-EM structure of the Mycobacterium smegmatis 70S ribosome in complex with hibernation factor Msmeg1130 (Balon) and MsmegEF-Tu(GDP) (Composite structure 6) Type: RIBOSOME / Entity ID: #1-#59 / Source: NATURAL |
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Molecular weight | Value: 2.6 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 Details: 20 mM HEPES-KOH, 60 mM KCl, 10 mM MgCl2, 1 mM dithiothreitol |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 295 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40.12 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10161 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101909 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5o61 Accession code: 5o61 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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