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Open data
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Basic information
Entry | Database: PDB / ID: 5nd9 | ||||||||||||||||||
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Title | Hibernating ribosome from Staphylococcus aureus (Rotated state) | ||||||||||||||||||
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![]() | RIBOSOME / S.aureus / HPF / hibernation / 100S ribosome | ||||||||||||||||||
Function / homology | ![]() negative regulation of translational elongation / ribosomal small subunit binding / 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 ...negative regulation of translational elongation / ribosomal small subunit binding / 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 / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||||||||
![]() | Khusainov, I. / Vicens, Q. / Ayupov, R. / Usachev, K. / Myasnikov, A. / Simonetti, A. / Validov, S. / Kieffer, B. / Yusupova, G. / Yusupov, M. / Hashem, Y. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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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
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 204.9 KB | Display | |
Data in CIF | ![]() | 355.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3625MC ![]() 3624C ![]() 3638C ![]() 3639C ![]() 5nd8C ![]() 5nkoC 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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Components
-RNA chain , 3 types, 3 molecules aAB
#1: RNA chain | Mass: 503242.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 87201381 |
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#23: RNA chain | Mass: 946696.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: GenBank: 87201381 |
#24: RNA chain | Mass: 36692.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() 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) ![]() 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) ![]() References: UniProt: Q2FW12 |
#4: Protein | Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FXK6 |
#5: Protein | Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW23 |
#6: Protein | Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2G113 |
#7: Protein | Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P48940 |
#8: Protein | Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW20 |
#9: Protein | Mass: 14856.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW39 |
#10: Protein | Mass: 11600.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q931G5 |
#11: Protein | Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW31 |
#12: Protein | Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: P0A0H0 |
#13: Protein | Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW30 |
#14: Protein | Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW19 |
#15: Protein | Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2G2Q1 |
#16: Protein | Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FZ45 |
#17: Protein | Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW15 |
#18: Protein | Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2G111 |
#19: Protein | Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FW10 |
#20: Protein | Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q2FXY6 |
#21: Protein | Mass: 6994.267 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() 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.) ![]() Gene: hpf, SAOUHSC_00767 / Production host: ![]() ![]() |
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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 |
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Sample preparation
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Molecular weight | Value: 2.5 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||
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 |
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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: ![]() |
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 |
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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 | ||||||||||||||||||||||||||||||||||||
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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