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Yorodumi- PDB-7qi4: Human mitochondrial ribosome at 2.2 A resolution (bound to partly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qi4 | ||||||||||||||||||
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Title | Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA) | ||||||||||||||||||
Components |
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Keywords | RIBOSOME / mitochondrial translation / tRNA / mRNA / 2Fe-2S clusters / polyamines / rRNA modifications / post-translation modifications / cryo EM | ||||||||||||||||||
Function / homology | Function and homology information mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / positive regulation of mitochondrial translation / Mitochondrial translation termination / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / RNA processing / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / small ribosomal subunit rRNA binding / fibrillar center / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / regulation of translation / double-stranded RNA binding / cell junction / small ribosomal subunit / 5S rRNA binding / endonuclease activity / nuclear membrane / mitochondrial inner membrane / cell population proliferation / tRNA binding / negative regulation of translation / rRNA binding / nuclear body / ribosome / mitochondrial matrix / structural constituent of ribosome / cell cycle / translation / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mRNA binding / intracellular membrane-bounded organelle / synapse / apoptotic process / GTP binding / nucleolus / positive regulation of DNA-templated transcription / mitochondrion / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.21 Å | ||||||||||||||||||
Authors | Singh, V. / Itoh, Y. / Amunts, A. | ||||||||||||||||||
Funding support | Sweden, European Union, 5items
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Citation | Journal: bioRxiv / Year: 2023 Title: Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications. Authors: Vivek Singh / Yuzuru Itoh / Samuel Del'Olio / Asem Hassan / Andreas Naschberger / Rasmus Kock Flygaard / Yuko Nobe / Keiichi Izumikawa / Shintaro Aibara / Juni Andréll / Paul C Whitford / ...Authors: Vivek Singh / Yuzuru Itoh / Samuel Del'Olio / Asem Hassan / Andreas Naschberger / Rasmus Kock Flygaard / Yuko Nobe / Keiichi Izumikawa / Shintaro Aibara / Juni Andréll / Paul C Whitford / Antoni Barrientos / Masato Taoka / Alexey Amunts Abstract: The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with ...The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA . The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transition in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide the most complete description so far of the structure and function of the human mitoribosome. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qi4.cif.gz | 7.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7qi4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/7qi4 ftp://data.pdbj.org/pub/pdb/validation_reports/qi/7qi4 | HTTPS FTP |
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-Related structure data
Related structure data | 13980MC 7qi5C 7qi6C 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 , 7 types, 7 molecules AAAwAxAzABAy
#1: RNA chain | Mass: 306218.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
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#32: RNA chain | Mass: 6971.210 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#33: RNA chain | Mass: 22354.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#34: RNA chain | Mass: 10826.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#35: RNA chain | Mass: 499786.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: GenBank: 1563835895 |
#36: RNA chain | Mass: 22989.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: GenBank: NC_012920.1 |
#89: RNA chain | Mass: 16669.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
+28S ribosomal protein ... , 26 types, 26 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPARASATAUAVAWAXAYAZA0A1
-Protein , 7 types, 7 molecules AQA2A3A4opq
#17: Protein | Mass: 10806.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: A0A2J8VEN6 |
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#29: Protein | Mass: 13540.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96BP2 |
#30: Protein | Mass: 22395.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NWT8 |
#31: Protein | Mass: 78648.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY7 |
#82: 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 |
#83: 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 |
#84: 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 |
+39S ribosomal protein ... , 49 types, 54 molecules DEFHIJKLMNOPQRSTUVWXYZ01234567...
-Non-polymers , 12 types, 8277 molecules
#90: Chemical | ChemComp-NAD / | ||||||||||||||||||
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#91: Chemical | ChemComp-SPM / | ||||||||||||||||||
#92: Chemical | ChemComp-SPD / #93: Chemical | ChemComp-MG / #94: Chemical | ChemComp-K / #95: Chemical | #96: Chemical | #97: Chemical | ChemComp-ATP / | #98: Chemical | ChemComp-GDP / | #99: Chemical | ChemComp-PUT / | #100: Chemical | ChemComp-VAL / | #101: 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 |
-Sample preparation
Component | Name: Human mitochondrial ribosome / Type: RIBOSOME / Entity ID: #1-#33, #89, #34-#35, #37-#88 / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2800 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 509691 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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