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Yorodumi- PDB-6ydp: 55S mammalian mitochondrial ribosome with mtEFG1 and P site fMet-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ydp | ||||||||||||
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Title | 55S mammalian mitochondrial ribosome with mtEFG1 and P site fMet-tRNAMet (POST) | ||||||||||||
Components |
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Keywords | TRANSLATION / Mitochondria / 55S ribosome / mtEFG1 / Elongation | ||||||||||||
Function / homology | Function and homology information Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / : / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly ...Hormone ligand-binding receptors / gonadotropin-releasing hormone receptor binding / gonadotropin hormone-releasing hormone activity / G alpha (q) signalling events / Mitochondrial translation elongation / Mitochondrial translation termination / : / mitochondrial translational termination / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation elongation / ribonuclease III activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / organelle membrane / RNA processing / translation elongation factor activity / rescue of stalled ribosome / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / double-stranded RNA binding / large ribosomal subunit / regulation of translation / cell junction / small ribosomal subunit / nuclear membrane / negative regulation of translation / rRNA binding / nuclear body / ribosome / mitochondrial matrix / structural constituent of ribosome / cell cycle / ribonucleoprotein complex / translation / protein domain specific binding / nucleotide binding / mRNA binding / intracellular membrane-bounded organelle / GTPase activity / 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) Sus scrofa (pig) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||||||||
Authors | Kummer, E. / Ban, N. | ||||||||||||
Funding support | Switzerland, 3items
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Citation | Journal: EMBO J / Year: 2020 Title: Structural insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1. Authors: Eva Kummer / Nenad Ban / Abstract: Mitochondria are eukaryotic organelles of bacterial origin where respiration takes place to produce cellular chemical energy. These reactions are catalyzed by the respiratory chain complexes located ...Mitochondria are eukaryotic organelles of bacterial origin where respiration takes place to produce cellular chemical energy. These reactions are catalyzed by the respiratory chain complexes located in the inner mitochondrial membrane. Notably, key components of the respiratory chain complexes are encoded on the mitochondrial chromosome and their expression relies on a dedicated mitochondrial translation machinery. Defects in the mitochondrial gene expression machinery lead to a variety of diseases in humans mostly affecting tissues with high energy demand such as the nervous system, the heart, or the muscles. The mitochondrial translation system has substantially diverged from its bacterial ancestor, including alterations in the mitoribosomal architecture, multiple changes to the set of translation factors and striking reductions in otherwise conserved tRNA elements. Although a number of structures of mitochondrial ribosomes from different species have been determined, our mechanistic understanding of the mitochondrial translation cycle remains largely unexplored. Here, we present two cryo-EM reconstructions of human mitochondrial elongation factor G1 bound to the mammalian mitochondrial ribosome at two different steps of the tRNA translocation reaction during translation elongation. Our structures explain the mechanism of tRNA and mRNA translocation on the mitoribosome, the regulation of mtEFG1 activity by the ribosomal GTPase-associated center, and the basis of decreased susceptibility of mtEFG1 to the commonly used antibiotic fusidic acid. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ydp.cif.gz | 4.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ydp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ydp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/6ydp ftp://data.pdbj.org/pub/pdb/validation_reports/yd/6ydp | HTTPS FTP |
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-Related structure data
Related structure data | 10778MC 6ydwC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Mitochondrial ribosomal protein ... , 39 types, 45 molecules B0BUBVBaBbBcBeBgBiBjBmBnBtB1BxABACAEAGAJALANARAaAcAdAeB2AhAk...
+Protein , 37 types, 37 molecules BWBXBYBfBhBlBoBpBqBuBvAFAIAKAOAQAUAbAfAgAiAjAmAnAoB3B4B5B6B9...
-Uncharacterized ... , 2 types, 2 molecules BdBR
#10: Protein | Mass: 24075.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZP98 |
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#85: Protein | Mass: 19268.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RMQ4 |
-39S ribosomal protein ... , 2 types, 2 molecules BkBw
#17: Protein | Mass: 29942.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480J9Z6 |
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#27: Protein | Mass: 49100.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480QIM3 |
-RNA chain , 4 types, 5 molecules AABAAVAXBB
#30: RNA chain | Mass: 5350865.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #46: RNA chain | | Mass: 22664.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1208989970 #47: RNA chain | | Mass: 1892.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #73: RNA chain | | Mass: 23402.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 76262549 |
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-28S ribosomal protein ... , 2 types, 2 molecules APAp
#42: Protein | Mass: 15182.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JTD7 |
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#64: Protein | Mass: 29220.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q767K8 |
-Protein/peptide , 1 types, 1 molecules AZ
#48: Protein/peptide | Mass: 1297.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) |
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-Non-polymers , 8 types, 345 molecules
#88: Chemical | ChemComp-MG / #89: Chemical | ChemComp-ZN / #90: Chemical | #91: Chemical | ChemComp-FME / | #92: Chemical | ChemComp-GTP / | #93: Chemical | #94: Chemical | ChemComp-GNP / | #95: 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 |
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.6 | ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.017 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
-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: OTHER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software | Name: EPU / Version: 1.9.0.30REL / Category: image acquisition |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97764 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |