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Yorodumi- PDB-8wi9: Cryo- EM structure of Mycobacterium smegmatis 30S ribosomal subun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wi9 | ||||||
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Title | Cryo- EM structure of Mycobacterium smegmatis 30S ribosomal subunit (body 2) of 70S ribosome, bS1 and RafH. | ||||||
Components |
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Keywords | RIBOSOME / protein synthesis / Mycobacterium smegmatis / hibernation promotion factor / HPF / RafH / hypoxia stress / Cryo- EM / Single particle reconstruction | ||||||
Function / homology | Function and homology information primary metabolic process / nucleotidyltransferase activity / regulation of translation / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...primary metabolic process / nucleotidyltransferase activity / regulation of translation / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / zinc ion binding / 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
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wi9.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8wi9.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8wi9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/8wi9 ftp://data.pdbj.org/pub/pdb/validation_reports/wi/8wi9 | HTTPS FTP |
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-Related structure data
Related structure data | 37561MC 8whxC 8whyC 8wi7C 8wi8C 8wibC 8wicC 8widC 8wifC 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
+30S ribosomal protein ... , 21 types, 21 molecules bvdefghijklmnopqrstuc
-RNA chain / Protein/peptide / Protein , 3 types, 3 molecules axw
#1: RNA chain | Mass: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: mc(2)155 / References: GenBank: 118168627 |
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#23: Protein/peptide | Mass: 1342.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: mc(2)155 / References: UniProt: A0R215 |
#24: Protein | Mass: 29898.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Gene: MSMEG_3935 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0QZ86 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: mc(2)155 | ||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C41(DE3) / Plasmid: pET28a(+) | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
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 | Cryogen name: ETHANE / Humidity: 100 % |
-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: OTHER |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm / Alignment procedure: NONE |
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 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 12343 |
-Processing
EM software |
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CTF correction | Details: CTF correction in RELION 3.1.4 / Type: NONE | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1202461 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: OTHER / Num. of particles: 110934 / Details: Ad-hoc low pass filter 3.5 Angstrom / Num. of class averages: 3 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8WHX Accession code: 8WHX / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||
Refine LS restraints |
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