[English] 日本語
Yorodumi- PDB-8wic: Cryo- EM structure of Mycobacterium smegmatis 50S ribosomal subun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wic | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo- EM structure of Mycobacterium smegmatis 50S ribosomal subunit (body 1) of 70S ribosome, E- tRNA and RafH. | ||||||
Components |
| ||||||
Keywords | RIBOSOME / protein synthesis / Mycobacterium smegmatis / hibernation promotion factor / HPF / RafH / hypoxia stress / Cryo- EM / Single particle reconstruction | ||||||
Function / homology | Function and homology information large ribosomal subunit / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Kumar, N. / Sharma, S. / Kaushal, P.S. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2024 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8wic.cif.gz | 2 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8wic.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 8wic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/8wic ftp://data.pdbj.org/pub/pdb/validation_reports/wi/8wic | HTTPS FTP |
---|
-Related structure data
Related structure data | 37563MC 8whxC 8whyC 8wi7C 8wi8C 8wi9C 8wibC 8widC 8wifC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
+50S ribosomal protein ... , 26 types, 26 molecules EFGHIJMNOQRSTUVWXZ12356784
-RNA chain , 3 types, 3 molecules ABC
#27: RNA chain | Mass: 1011834.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) |
---|---|
#28: RNA chain | Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: GenBank: 118168627 |
#29: RNA chain | Mass: 24465.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 70S ribosome + RafH protein / Type: RIBOSOME / Entity ID: all / Source: NATURAL |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155 |
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: NO / Vitrification applied: YES |
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 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm |
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: 110934 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: CTF correction in Relion / Type: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: OTHER / Num. of particles: 44299 / Details: Ad-hoc low pass filter 3.5 Angstrom / Num. of class averages: 1 / 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 |
|