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Yorodumi- PDB-8rdv: Cryo-EM structure of P. urativorans 70S ribosome in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rdv | ||||||
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Title | Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factor Balon, mRNA and P-site tRNA (structure 2). | ||||||
Components |
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Keywords | RIBOSOME / Hibernation factor / Dormancy / Balon | ||||||
Function / homology | Function and homology information guanosine tetraphosphate binding / translation elongation factor activity / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome ...guanosine tetraphosphate binding / translation elongation factor activity / large ribosomal subunit / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Psychrobacter urativorans (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Helena-Bueno, K. / Rybak, M.Y. / Gagnon, M.G. / Hill, C.H. / Melnikov, S.V. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nature / Year: 2024 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. #1: Journal: Biorxiv / Year: 2023 Title: A bacterial ribosome hibernation factor with evolutionary connections to eukaryotic protein synthesis Authors: Helena-Bueno, K. / Ekemezie, C.L. / Brown, C.R. / Basle, A. / Blaza, J.N. / Hill, C.H. / Melnikov, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rdv.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8rdv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8rdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/8rdv ftp://data.pdbj.org/pub/pdb/validation_reports/rd/8rdv | HTTPS FTP |
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-Related structure data
Related structure data | 19076MC 8rd8C 8rdwC 8v9jC 8v9kC 8v9lC 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 , 2 types, 2 molecules BH
#1: Protein | Mass: 41159.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8U3 |
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#3: Protein | Mass: 43108.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U5B4 |
-Small ribosomal subunit protein ... , 20 types, 20 molecules FR3A4E5L6FGHKOLMMSPBQGSCTKUNVJYQZPjDmTo
#2: Protein | Mass: 14278.470 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T6M9 |
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#5: Protein | Mass: 8973.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MK69 |
#6: Protein | Mass: 29465.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TFJ4 |
#7: Protein | Mass: 18192.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8J0 |
#8: Protein | Mass: 13753.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U4C3 |
#18: Protein | Mass: 15839.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U628 |
#22: Protein | Mass: 11777.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8P8 |
#23: Protein | Mass: 10218.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TF29 |
#24: Protein | Mass: 13244.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M5MJL8 |
#26: Protein | Mass: 10336.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TUJ8 |
#27: Protein | Mass: 14086.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U618 |
#29: Protein | Mass: 17760.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8N5 |
#30: Protein | Mass: 27120.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T6V9 |
#31: Protein | Mass: 13676.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M3V8P6 |
#32: Protein | Mass: 8548.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4SY21 |
#35: Protein | Mass: 11635.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TE68 |
#36: Protein | Mass: 10362.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4U401 |
#46: Protein | Mass: 9955.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T275 |
#49: Protein | Mass: 24279.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4TE52 |
#51: Protein | Mass: 9980.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: UniProt: A0A0M4T3R2 |
-RNA chain , 3 types, 3 molecules Z2D8iN
#4: RNA chain | Mass: 933562.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) |
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#10: RNA chain | Mass: 36948.945 Da / Num. of mol.: 1 Mutation: Contains an inserted nucleotide U at position 85 and a point mutation C88A compared to the genome-based predicted sequences. Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: GenBank: 930356181 |
#56: RNA chain | Mass: 514949.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psychrobacter urativorans (bacteria) / References: GenBank: 930356181 |
+Large ribosomal subunit protein ... , 29 types, 29 molecules F7E9aAMBUCWDXERFVHTIfJPOGRYWIXBaQbNcKdJeAfLgdhOibkClSnepC1
-Heterogenous ... , 2 types, 2 molecules VY
#53: RNA chain | Mass: 23267.762 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Psychrobacter urativorans (bacteria) |
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#54: RNA chain | Mass: 1792.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Psychrobacter urativorans (bacteria) |
-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: Ribosomes isolated from ice-treated cultures of Psychrobacter urativorans. Type: RIBOSOME / Entity ID: #1-#55 / Source: NATURAL |
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Source (natural) | Organism: Psychrobacter urativorans (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30469 / Symmetry type: POINT |