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Yorodumi- PDB-8wi7: Cryo- EM structure of Mycobacterium smegmatis 70S ribosome, bS1 a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wi7 | ||||||
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Title | Cryo- EM structure of Mycobacterium smegmatis 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 negative regulation of translational elongation / ribosomal small subunit binding / nucleotidyltransferase activity / large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding ...negative regulation of translational elongation / ribosomal small subunit binding / nucleotidyltransferase activity / 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 / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / metal ion binding / cytoplasm / cytosol 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 | 8wi7.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8wi7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8wi7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wi7_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8wi7_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8wi7_validation.xml.gz | 197.3 KB | Display | |
Data in CIF | 8wi7_validation.cif.gz | 351.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/8wi7 ftp://data.pdbj.org/pub/pdb/validation_reports/wi/8wi7 | HTTPS FTP |
-Related structure data
Related structure data | 37559MC 8whxC 8whyC 8wi8C 8wi9C 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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-Components
+50S ribosomal protein ... , 26 types, 26 molecules EFGHIJMNOQRSTUVWXZ12356784
-RNA chain , 3 types, 3 molecules ABa
#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) |
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#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: 495373.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: GenBank: 118168627 |
+30S ribosomal protein ... , 21 types, 21 molecules bvdefghijklmnopqrstuc
-Protein , 1 types, 1 molecules w
#51: 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) / Strain (production host): c41 (DE3) / References: UniProt: A0QZ86 |
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-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 / 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 |
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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: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1800 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 1.34 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Details: CTF correction in Relion / Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110934 / 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 |