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Yorodumi- PDB-6ydw: 55S mammalian mitochondrial ribosome with mtEFG1 and two tRNAMet ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ydw | ||||||||||||
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Title | 55S mammalian mitochondrial ribosome with mtEFG1 and two tRNAMet (TI-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 transcription / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity ...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 transcription / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / organelle membrane / mitochondrial translation / positive regulation of proteolysis / ribosomal small subunit binding / translation elongation factor activity / RNA processing / rescue of stalled ribosome / cell junction / large ribosomal subunit / double-stranded RNA binding / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / nuclear membrane / cytosolic large ribosomal subunit / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / translation / ribonucleoprotein complex / protein domain specific binding / GTPase activity / mRNA binding / nucleotide binding / synapse / positive regulation of DNA-templated transcription / nucleolus / GTP binding / apoptotic process / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 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 | 6ydw.cif.gz | 4.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ydw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6ydw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ydw_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 6ydw_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 6ydw_validation.xml.gz | 380.6 KB | Display | |
Data in CIF | 6ydw_validation.cif.gz | 623.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yd/6ydw ftp://data.pdbj.org/pub/pdb/validation_reports/yd/6ydw | HTTPS FTP |
-Related structure data
Related structure data | 10779MC 6ydpC 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
+Uncharacterized ... , 22 types, 22 molecules AIBWBXBYBdBfBhBoBqBuBvAFB3B4B5B6BDBNBOBPBQBR
+Mitochondrial ribosomal protein ... , 39 types, 45 molecules BTBUBVBaBbBcBeBgBiBjBmBnBtB0BxABACAEAGAJALANARAaAcAdAeB1AhAk...
-39S ribosomal protein ... , 2 types, 2 molecules BkBw
#18: 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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#29: Protein | Mass: 49100.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480QIM3 |
-Protein , 17 types, 17 molecules BlBpAKAOAQAUAbAfAgAiAjAmAnAoB9BCBE
#19: Protein | Mass: 18957.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0R4J8D6 |
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#23: Protein | Mass: 12015.747 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A341D604 |
#38: Protein | Mass: 20841.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJJ6 |
#41: Protein | Mass: 27411.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BMP0 |
#43: Protein | Mass: 14452.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RIU0 |
#45: Protein | Mass: 10682.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZNB3 |
#50: Protein | Mass: 21666.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AEW3 |
#55: Protein | Mass: 21014.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0M3KL56 |
#56: Protein | Mass: 46966.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LS10 |
#58: Protein | Mass: 12544.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S8G3 |
#59: Protein | Mass: 25843.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AVS9 |
#61: Protein | Mass: 13561.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SU49 |
#62: Protein | Mass: 22843.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B3R8 |
#63: Protein | Mass: 78518.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 201-234 built as poly-Ala / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GKS8 |
#73: Protein | Mass: 10841.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287A731 |
#75: Protein | Mass: 80054.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: mtEFG1 residues 40-751 including an N-terminal SGGSGSGSSG-linker Source: (gene. exp.) Homo sapiens (human) / Gene: GFM1, EFG, EFG1, GFM / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RP9 |
#77: Protein | Mass: 38427.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A140UHW4 |
-RNA chain , 4 types, 6 molecules AABAAVAYAXBB
#31: RNA chain | Mass: 5350865.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 347448639 #46: RNA chain | Mass: 22664.498 Da / Num. of mol.: 2 / 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) #74: 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, 343 molecules
#88: Chemical | ChemComp-MG / #89: Chemical | ChemComp-ZN / #90: Chemical | #91: Chemical | ChemComp-FME / | #92: Chemical | ChemComp-GTP / | #93: Chemical | ChemComp-5GP / | #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 | Value: 2.8 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||
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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12858 / Symmetry type: POINT |
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |