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- PDB-7p2e: Human mitochondrial ribosome small subunit in complex with IF3, G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p2e | ||||||||||||
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Title | Human mitochondrial ribosome small subunit in complex with IF3, GMPPMP and streptomycin | ||||||||||||
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![]() | RIBOSOME / Initiation factor 3 / translation / antibiotic / streptomycin | ||||||||||||
Function / homology | ![]() mitochondrial translational initiation / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / ribosome disassembly / negative regulation of mitotic nuclear division ...mitochondrial translational initiation / mitochondrial ribosome binding / translation factor activity, RNA binding / mitochondrial ribosome assembly / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / ribosome disassembly / negative regulation of mitotic nuclear division / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / Mitochondrial protein degradation / translation initiation factor activity / apoptotic signaling pathway / fibrillar center / cell junction / ribosome binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / cytosolic small ribosomal subunit / cell population proliferation / mitochondrial inner membrane / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleolus / GTP binding / mitochondrion / RNA binding / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||||||||
![]() | Itoh, Y. / Khawaja, A. / Singh, V. / Rorbach, J. / Amunts, A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules. Authors: Yuzuru Itoh / Vivek Singh / Anas Khawaja / Andreas Naschberger / Minh Duc Nguyen / Joanna Rorbach / Alexey Amunts / ![]() Abstract: The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was ...The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was shown to be coupled with a bilateral decreased visual acuity. Previously, we reported mitochondria-specific protein aspects of the mitoribosome, and in this article we present a 2.4-Å resolution structure of the small subunit in a complex with the anti-tuberculosis drug streptomycin that reveals roles of non-protein components. We found iron-sulfur clusters that are coordinated by different mitoribosomal proteins, nicotinamide adenine dinucleotide (NAD) associated with rRNA insertion, and posttranslational modifications. This is the first evidence of inter-protein coordination of iron-sulfur, and the finding of iron-sulfur clusters and NAD as fundamental building blocks of the mitoribosome directly links to mitochondrial disease and aging. We also report details of streptomycin interactions, suggesting that the mitoribosome-bound streptomycin is likely to be in hydrated gem-diol form and can be subjected to other modifications by the cellular milieu. The presented approach of adding antibiotics to cultured cells can be used to define their native structures in a bound form under more physiological conditions, and since streptomycin is a widely used drug for treatment, the newly resolved features can serve as determinants for targeting. | ||||||||||||
History |
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Structure visualization
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 | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 164.5 KB | Display | |
Data in CIF | ![]() | 285.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 13170MC 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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1 |
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Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 306547.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
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+28S ribosomal protein ... , 27 types, 27 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ01
-Protein , 4 types, 4 molecules 2348
#29: Protein | Mass: 13409.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
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#30: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
#31: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
#32: Protein | Mass: 32545.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Natural variant Thr68Ile and Phe263Leu / Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 10 types, 3176 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/5I0.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/5I0.gif)
![](data/chem/img/K.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/GNP.gif)
![](data/chem/img/HOH.gif)
#33: Chemical | ChemComp-NAD / | ||||||||||||
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#34: Chemical | ChemComp-SPM / | ||||||||||||
#35: Chemical | ChemComp-5I0 / [( | ||||||||||||
#36: Chemical | ChemComp-K / #37: Chemical | ChemComp-MG / #38: Chemical | ChemComp-ZN / | #39: Chemical | #40: Chemical | ChemComp-ATP / | #41: Chemical | ChemComp-GNP / | #42: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K |
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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 / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 31773 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 20 / Used frames/image: 1-20 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2487123 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 885199 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6RW4 Accession code: 6RW4 / Source name: PDB / Type: experimental model |