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Yorodumi- PDB-7pnw: Mouse mitochondrial ribosome small subunit lacking m5U modification -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pnw | ||||||||||||
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Title | Mouse mitochondrial ribosome small subunit lacking m5U modification | ||||||||||||
Components |
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Keywords | RIBOSOME / Small subunit / mitochondrion | ||||||||||||
Function / homology | Function and homology information Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial ribosome binding / anaphase-promoting complex / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial ribosome binding / anaphase-promoting complex / mitochondrial ribosome assembly / positive regulation of mitochondrial translation / mitochondrial small ribosomal subunit / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / apoptotic mitochondrial changes / ribosomal small subunit binding / fibrillar center / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / cell junction / regulation of translation / nuclear membrane / cell population proliferation / mitochondrial inner membrane / tRNA binding / rRNA binding / ribosome / protein ubiquitination / mitochondrial matrix / structural constituent of ribosome / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å | ||||||||||||
Authors | Itoh, Y. / Khawaja, A. / Laptev, I. / Sergiev, P. / Rorbach, J. / Amunts, A. | ||||||||||||
Funding support | European Union, 3items
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Citation | Journal: Nature / Year: 2022 Title: Mechanism of mitoribosomal small subunit biogenesis and preinitiation. Authors: Yuzuru Itoh / Anas Khawaja / Ivan Laptev / Miriam Cipullo / Ilian Atanassov / Petr Sergiev / Joanna Rorbach / Alexey Amunts / Abstract: Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) ...Mitoribosomes are essential for the synthesis and maintenance of bioenergetic proteins. Here we use cryo-electron microscopy to determine a series of the small mitoribosomal subunit (SSU) intermediates in complex with auxiliary factors, revealing a sequential assembly mechanism. The methyltransferase TFB1M binds to partially unfolded rRNA h45 that is promoted by RBFA, while the mRNA channel is blocked. This enables binding of METTL15 that promotes further rRNA maturation and a large conformational change of RBFA. The new conformation allows initiation factor mtIF3 to already occupy the subunit interface during the assembly. Finally, the mitochondria-specific ribosomal protein mS37 (ref. ) outcompetes RBFA to complete the assembly with the SSU-mS37-mtIF3 complex that proceeds towards mtIF2 binding and translation initiation. Our results explain how the action of step-specific factors modulate the dynamic assembly of the SSU, and adaptation of a unique protein, mS37, links the assembly to initiation to establish the catalytic human mitoribosome. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pnw.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7pnw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7pnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/7pnw ftp://data.pdbj.org/pub/pdb/validation_reports/pn/7pnw | HTTPS FTP |
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-Related structure data
Related structure data | 13554MC 7pntC 7pnuC 7pnvC 7pnxC 7pnyC 7pnzC 7po0C 7po1C 7po2C 7po3C 7po4C 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
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 306877.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 |
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+28S ribosomal protein ... , 27 types, 27 molecules BCDEFGHIJKLMNOPQRSTUVWXYZ01
-Protein , 3 types, 3 molecules 234
#29: Protein | Mass: 13543.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9CQA6 |
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#30: Protein | Mass: 23345.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q9DCJ7 |
#31: Protein | Mass: 77890.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Mus musculus (house mouse) / Cell line: NS0 / References: UniProt: Q14C51 |
-Non-polymers , 6 types, 854 molecules
#32: Chemical | ChemComp-MG / #33: Chemical | ChemComp-K / #34: Chemical | ChemComp-ZN / | #35: Chemical | #36: Chemical | ChemComp-ATP / | #37: Water | ChemComp-HOH / | |
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-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 |
-Sample preparation
Component | Name: Small subunit of human mitochondrial ribosome / Type: RIBOSOME / Entity ID: #1-#31 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Mus musculus (house mouse) | ||||||||||||||||||||||||||||||
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 mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 297 K |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 800 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: 31 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 26468 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 20 / Used frames/image: 1-20 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3076615 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44121 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6RW4 Accession code: 6RW4 / Source name: PDB / Type: experimental model |