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Yorodumi- PDB-7po4: Assembly intermediate of human mitochondrial ribosome large subun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7po4 | ||||||||||||
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Title | Assembly intermediate of human mitochondrial ribosome large subunit (largely unfolded rRNA with MALSU1, L0R8F8 and ACP) | ||||||||||||
Components |
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Keywords | RIBOSOME / Small subunit / mitochondrion / biogenesis / maturation | ||||||||||||
Function / homology | Function and homology information negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial transcription / mitochondrial translational elongation ...negative regulation of mitochondrial translation / mitochondrial large ribosomal subunit assembly / Complex I biogenesis / negative regulation of ribosome biogenesis / protein lipoylation / Mitochondrial Fatty Acid Beta-Oxidation / rRNA import into mitochondrion / Respiratory electron transport / mitochondrial transcription / mitochondrial translational elongation / mitochondrial translational termination / iron-sulfur cluster assembly complex / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / mitochondrial large ribosomal subunit binding / Glyoxylate metabolism and glycine degradation / mitochondrial fission / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / [2Fe-2S] cluster assembly / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / iron-sulfur cluster assembly / mitochondrial ribosome / mitochondrial translation / ribosomal large subunit binding / : / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / mitochondrial respiratory chain complex I assembly / acyl binding / acyl carrier activity / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / aerobic respiration / rescue of stalled ribosome / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / fatty acid binding / mitochondrial membrane / fibrillar center / fatty acid biosynthetic process / double-stranded RNA binding / cell junction / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / endonuclease activity / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / nucleotide binding / mRNA binding / apoptotic process / synapse / calcium ion binding / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.56 Å | ||||||||||||
Authors | Itoh, Y. / Khawaja, A. / 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 | 7po4.cif.gz | 3.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7po4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7po4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7po4_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7po4_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7po4_validation.xml.gz | 220 KB | Display | |
Data in CIF | 7po4_validation.cif.gz | 384.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/7po4 ftp://data.pdbj.org/pub/pdb/validation_reports/po/7po4 | HTTPS FTP |
-Related structure data
Related structure data | 13562MC 7pntC 7pnuC 7pnvC 7pnwC 7pnxC 7pnyC 7pnzC 7po0C 7po1C 7po2C 7po3C 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 , 2 types, 2 molecules AB
#1: RNA chain | Mass: 500671.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
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#2: RNA chain | Mass: 22989.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
+39S ribosomal protein ... , 47 types, 52 molecules DEFHIJKLMNOPQRSTUVWXYZ01235678...
-Protein , 6 types, 6 molecules opqzazbzc
#47: Protein | Mass: 12292.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BQC6 |
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#48: Protein | Mass: 23674.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q14197, peptidyl-tRNA hydrolase |
#49: Protein | Mass: 25426.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TAE8 |
#53: Protein | Mass: 26203.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EH3 |
#54: Protein | Mass: 8460.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: L0R8F8 |
#55: Protein | Mass: 17434.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: O14561 |
-Non-polymers , 6 types, 2589 molecules
#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-K / #58: Chemical | ChemComp-ZN / | #59: Chemical | ChemComp-FES / | #60: Chemical | ChemComp-8Q1 / | #61: 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: Assembly intermediate of the large subunit of human mitochondrial ribosome Type: RIBOSOME / Entity ID: #1-#55 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||
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 R2/2 | ||||||||||||||||||||||||||||||
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 FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 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: 5 sec. / Electron dose: 31 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 20583 |
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: 1073141 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180400 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6ZM6 Accession code: 6ZM6 / Source name: PDB / Type: experimental model |