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Yorodumi- PDB-5nd8: Hibernating ribosome from Staphylococcus aureus (Unrotated state) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nd8 | ||||||||||||||||||
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Title | Hibernating ribosome from Staphylococcus aureus (Unrotated state) | ||||||||||||||||||
Components |
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Keywords | RIBOSOME / S.aureus / HPF / hibernation / 100S ribosome | ||||||||||||||||||
Function / homology | Function and homology information negative regulation of translational elongation / ribosomal small subunit binding / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity ...negative regulation of translational elongation / ribosomal small subunit binding / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Staphylococcus aureus (bacteria) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||
Authors | Khusainov, I. / Vicens, Q. / Ayupov, R. / Usachev, K. / Myasnikov, A. / Simonetti, A. / Validov, S. / Kieffer, B. / Yusupova, G. / Yusupov, M. / Hashem, Y. | ||||||||||||||||||
Funding support | France, Russian Federation, 5items
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Citation | Journal: EMBO J / Year: 2017 Title: Structures and dynamics of hibernating ribosomes from mediated by intermolecular interactions of HPF. Authors: Iskander Khusainov / Quentin Vicens / Rustam Ayupov / Konstantin Usachev / Alexander Myasnikov / Angelita Simonetti / Shamil Validov / Bruno Kieffer / Gulnara Yusupova / Marat Yusupov / Yaser Hashem / Abstract: In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of ...In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy. Our reconstructions reveal that the N-terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species. The C-terminal domain (CTD) of SaHPF protrudes out of each ribosome in order to mediate dimerization. Using NMR, we characterized the interactions at the CTD-dimer interface. Secondary interactions are provided by helix 26 of the 16S ribosomal RNA We also show that ribosomes in the 100S particle adopt both rotated and unrotated conformations. Overall, our work illustrates a specific mode of ribosome dimerization by long HPF, a finding that may help improve the selectivity of antimicrobials. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5nd8.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5nd8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5nd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nd8_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5nd8_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5nd8_validation.xml.gz | 195.7 KB | Display | |
Data in CIF | 5nd8_validation.cif.gz | 345 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/5nd8 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/5nd8 | HTTPS FTP |
-Related structure data
Related structure data | 3624MC 3625C 3638C 3639C 5nd9C 5nkoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules aAB
#1: RNA chain | Mass: 500464.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: GenBank: 87201381 |
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#23: RNA chain | Mass: 945058.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: GenBank: 87201381 |
#24: RNA chain | Mass: 36692.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: GenBank: 87201381 |
-30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu
#2: Protein | Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FZ25 |
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#3: Protein | Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FW12 |
#4: Protein | Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FXK6 |
#5: Protein | Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FW23 |
#6: Protein | Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2G113 |
#7: Protein | Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: P48940 |
#8: Protein | Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FW20 |
#9: Protein | Mass: 14856.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FW39 |
#10: Protein | Mass: 11600.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: A7X5G6 |
#11: Protein | Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FW31 |
#12: Protein | Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: P0A0H0 |
#13: Protein | Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FW30 |
#14: Protein | Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FW19 |
#15: Protein | Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2G2Q1 |
#16: Protein | Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FZ45 |
#17: Protein | Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FW15 |
#18: Protein | Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2G111 |
#19: Protein | Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FW10 |
#20: Protein | Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FXY6 |
#21: Protein | Mass: 6994.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325) (bacteria) References: UniProt: Q2FXZ7 |
-Protein , 1 types, 1 molecules v
#22: Protein | Mass: 22244.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria) Gene: hpf, SAOUHSC_00767 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q2G055 |
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+50S ribosomal protein ... , 28 types, 28 molecules DEFGHMNOPQRSTUVWXYZ012345678
-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 |
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Molecular weight | Value: 2.5 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) | ||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: 5 mM Hepes-KOH pH 7.5 50 mM KCl 10 mM NH4Cl 10 mM Mg(OAc)2 1 mM DTT | ||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER | ||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot force 5, blot waiting time 30 s |
-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: DARK FIELD |
Image recording | Average exposure time: 1 sec. / Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 |
Image scans | Movie frames/image: 17 / Used frames/image: 2-8 |
-Processing
Software | Name: PHENIX / Version: 1.11_2567: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 348000 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83000 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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