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Yorodumi- PDB-7qi6: Human mitochondrial ribosome in complex with mRNA, A/P- and P/E-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qi6 | ||||||||||||||||||
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Title | Human mitochondrial ribosome in complex with mRNA, A/P- and P/E-tRNAs at 2.98 A resolution | ||||||||||||||||||
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 transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / positive regulation of mitochondrial translation / microprocessor complex / Mitochondrial translation elongation ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial transcription / mitochondrial translational termination / mitochondrial translational elongation / mitochondrial ribosome assembly / translation release factor activity, codon nonspecific / positive regulation of mitochondrial translation / microprocessor complex / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / negative regulation of mitotic nuclear division / 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 / Mitochondrial protein degradation / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / fibrillar center / double-stranded RNA binding / small ribosomal subunit rRNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / nuclear membrane / endonuclease activity / cell population proliferation / tRNA binding / mitochondrial inner membrane / negative regulation of translation / nuclear body / rRNA binding / ribosome / mitochondrial matrix / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / intracellular membrane-bounded organelle / mRNA binding / nucleotide binding / synapse / GTP binding / nucleolus / apoptotic process / positive regulation of DNA-templated transcription / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å | ||||||||||||||||||
Authors | Singh, V. / Itoh, Y. / Amunts, A. | ||||||||||||||||||
Funding support | European Union, 5items
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Citation | Journal: Nat Commun / Year: 2024 Title: Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk. 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 ...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 us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions 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 a description of the structure and function of the human mitoribosome. #1: Journal: Nat Commun / Year: 2024 Title: Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk. 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 ...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 us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions 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 a description of the structure and function of the human mitoribosome. #2: 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 | 7qi6.cif.gz | 6.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7qi6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qi6_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 7qi6_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 7qi6_validation.xml.gz | 369.5 KB | Display | |
Data in CIF | 7qi6_validation.cif.gz | 640.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/7qi6 ftp://data.pdbj.org/pub/pdb/validation_reports/qi/7qi6 | HTTPS FTP |
-Related structure data
Related structure data | 13982MC 7qi4C 7qi5C 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 , 6 types, 6 molecules AAAzAwAxAB
#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) / References: GenBank: 1858624182 |
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#32: RNA chain | Mass: 10543.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#33: RNA chain | Mass: 21642.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: GenBank: 1896813690 |
#34: RNA chain | Mass: 22626.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) |
#35: RNA chain | Mass: 500727.125 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 |
+28S ribosomal protein ... , 26 types, 26 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPARASATAUAVAWAXAYAZA0A1
-Protein , 8 types, 8 molecules AQA2A3A4bopq
#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 |
#68: Protein | Mass: 23352.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N983 |
#80: 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 |
#81: 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 |
#82: 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 ... , 48 types, 53 molecules DEFIJKLMNOPRSTUVWXYZ0123456789...
-Non-polymers , 12 types, 3576 molecules
#89: Chemical | ChemComp-NAD / | ||||||||||||||||||
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#90: Chemical | ChemComp-SPM / | ||||||||||||||||||
#91: Chemical | ChemComp-SPD / #92: Chemical | ChemComp-K / #93: Chemical | ChemComp-MG / #94: Chemical | #95: Chemical | #96: Chemical | ChemComp-ATP / | #97: Chemical | ChemComp-GDP / | #98: Chemical | ChemComp-PUT / | #99: Chemical | ChemComp-VAL / | #100: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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-#67, #69-#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 FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20143 / Symmetry type: POINT | ||||||||||||||||||||||||
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