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- PDB-8wi8: Cryo- EM structure of Mycobacterium smegmatis 50S ribosomal subun... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8wi8 | ||||||
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Title | Cryo- EM structure of Mycobacterium smegmatis 50S ribosomal subunit (body 1) of 70S ribosome, bS1 and RafH. | ||||||
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Function / homology | ![]() large ribosomal subunit / large ribosomal subunit rRNA binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumar, N. / Sharma, S. / Kaushal, P.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH. Authors: Niraj Kumar / Shivani Sharma / Prem S Kaushal / ![]() Abstract: Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium ...Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium tuberculosis encounters hypoxia (low oxygen) as a major stress in the host macrophages, and upregulates the expression of RafH protein, which is crucial for its survival. The RafH, a dual domain HPF, an orthologue of bacterial long HPF (HPF), hibernates ribosome in 70S monosome form, whereas in other bacteria, the HPF induces 70S ribosome dimerization and hibernates its ribosome in 100S disome form. Here, we report the cryo- EM structure of M. smegmatis, a close homolog of M. tuberculosis, 70S ribosome in complex with the RafH factor at an overall 2.8 Å resolution. The N- terminus domain (NTD) of RafH binds to the decoding center, similarly to HPF NTD. In contrast, the C- terminus domain (CTD) of RafH, which is larger than the HPF CTD, binds to a distinct site at the platform binding center of the ribosomal small subunit. The two domain-connecting linker regions, which remain mostly disordered in earlier reported HPF structures, interact mainly with the anti-Shine Dalgarno sequence of the 16S rRNA. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 37560MC ![]() 8whxC ![]() 8whyC ![]() 8wi7C ![]() 8wi9C ![]() 8wibC ![]() 8wicC ![]() 8widC ![]() 8wifC 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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Links
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Assembly
Deposited unit | ![]()
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Components
+50S ribosomal protein ... , 26 types, 26 molecules EFGHIJMNOQRSTUVWXZ12356784
-RNA chain , 2 types, 2 molecules AB
#27: RNA chain | ![]() Mass: 1011834.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
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#28: RNA chain | ![]() Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: ![]() |
-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 + RafH protein / Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.4 / Details: 20mM HEPES, 20mM MgCl2, 100mM NH4Cl, 3mM DTT |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
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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: BRIGHT FIELD![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2 sec. / Electron dose: 1.34 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 12343 |
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Processing
EM software |
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CTF correction![]() | Details: CTF correction in Relion3.1.4 / Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1202461 | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110934 / Num. of class averages: 3 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Details: phenix.real_space_refinement | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8WHX Accession code: 8WHX / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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