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Yorodumi- PDB-6gb2: Unique features of mammalian mitochondrial translation initiation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gb2 | ||||||||||||
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Title | Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the 39S ribosomal subunit. | ||||||||||||
Components |
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Keywords | RIBOSOME / translation initiation / initiation factor IF2 / mitochondria / membrane targeting | ||||||||||||
Function / homology | Function and homology information Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / translation factor activity, RNA binding / ribosome disassembly / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial translational initiation / translation factor activity, RNA binding / ribosome disassembly / mitochondrial translational termination / mitochondrial transcription / mitochondrial translational elongation / translation release factor activity, codon nonspecific / microprocessor complex / Mitochondrial translation initiation / ribonuclease III activity / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / regulation of translational initiation / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / ribosomal small subunit binding / organelle membrane / RNA processing / rescue of stalled ribosome / translation initiation factor activity / double-stranded RNA binding / large ribosomal subunit / cell junction / rRNA binding / nuclear body / ribosome / structural constituent of ribosome / cell cycle / ribonucleoprotein complex / translation / protein domain specific binding / nucleotide binding / intracellular membrane-bounded organelle / GTPase activity / synapse / GTP binding / positive regulation of DNA-templated transcription / mitochondrion / 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: 3.2 Å | ||||||||||||
Authors | Kummer, E. / Leibundgut, M. / Boehringer, D. / Ban, N. | ||||||||||||
Funding support | Switzerland, 3items
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Citation | Journal: Nature / Year: 2018 Title: Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. Authors: Eva Kummer / Marc Leibundgut / Oliver Rackham / Richard G Lee / Daniel Boehringer / Aleksandra Filipovska / Nenad Ban / Abstract: Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation. The ...Mitochondria maintain their own specialized protein synthesis machinery, which in mammals is used exclusively for the synthesis of the membrane proteins responsible for oxidative phosphorylation. The initiation of protein synthesis in mitochondria differs substantially from bacterial or cytosolic translation systems. Mitochondrial translation initiation lacks initiation factor 1, which is essential in all other translation systems from bacteria to mammals. Furthermore, only one type of methionyl transfer RNA (tRNA) is used for both initiation and elongation, necessitating that the initiation factor specifically recognizes the formylated version of tRNA (fMet-tRNA). Lastly, most mitochondrial mRNAs do not possess 5' leader sequences to promote mRNA binding to the ribosome. There is currently little mechanistic insight into mammalian mitochondrial translation initiation, and it is not clear how mRNA engagement, initiator-tRNA recruitment and start-codon selection occur. Here we determine the cryo-EM structure of the complete translation initiation complex from mammalian mitochondria at 3.2 Å. We describe the function of an additional domain insertion that is present in the mammalian mitochondrial initiation factor 2 (mtIF2). By closing the decoding centre, this insertion stabilizes the binding of leaderless mRNAs and induces conformational changes in the rRNA nucleotides involved in decoding. We identify unique features of mtIF2 that are required for specific recognition of fMet-tRNA and regulation of its GTPase activity. Finally, we observe that the ribosomal tunnel in the initiating ribosome is blocked by insertion of the N-terminal portion of mitochondrial protein mL45, which becomes exposed as the ribosome switches to elongation mode and may have an additional role in targeting of mitochondrial ribosomes to the protein-conducting pore in the inner mitochondrial membrane. | ||||||||||||
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 | 6gb2.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6gb2.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6gb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/6gb2 ftp://data.pdbj.org/pub/pdb/validation_reports/gb/6gb2 | HTTPS FTP |
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-Related structure data
Related structure data | 4370MC 4368C 4369C 6gawC 6gazC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+Mitochondrial ribosomal protein ... , 42 types, 48 molecules CLDLELFLGLHLBLB0B1B2B5B6B7B8BDBFBIBJBKBNBOBPBQBRBSBTBUBVBWBX...
-'Mitochondrial ribosomal protein ... , 3 types, 3 molecules B3B4Bv
#5: Protein | ' Mass: 18585.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1STE5 |
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#6: Protein | ' Mass: 15156.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3L9J0 |
#52: Protein | ' Mass: 25815.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZXA6 |
-Protein , 8 types, 8 molecules B9BCBEBlBpBqBwBz
#11: Protein | Mass: 10841.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A287A731 |
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#14: Protein | Mass: 72811.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: mitochondrial / Source: (gene. exp.) Homo sapiens (human) / Gene: MTIF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P46199 |
#16: Protein | Mass: 38427.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) |
#44: Protein | Mass: 18957.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A0R4J8D6 |
#48: Protein | Mass: 12015.747 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver |
#49: Protein | Mass: 15957.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Unassigned residues have been built as poly-alanine. Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: I3LN63 |
#53: Protein | Mass: 49100.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) |
#55: Protein | Mass: 5846.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Unassigned secondary structure elements have been built as poly-alanine. Source: (natural) Sus scrofa (pig) / Organ: liver |
-RNA chain , 3 types, 3 molecules BABBAV
#12: RNA chain | Mass: 504852.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 33320725 |
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#13: 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 |
#56: RNA chain | Mass: 22664.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1208989970 |
-Non-polymers , 8 types, 228 molecules
#57: Chemical | ChemComp-MG / #58: Chemical | #59: Chemical | #60: Chemical | #61: Chemical | ChemComp-GSP / | #62: Chemical | ChemComp-NA / | #63: Chemical | ChemComp-FME / | #64: Water | ChemComp-HOH / | |
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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: 2.85 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.6 | ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.171 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: contains 55S mitochondrial ribosome, mitochondrial initiation factor 2, mitochondrial formyl-Met-tRNAMet and MT-CO3 mRNA | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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 FIELDBright-field microscopy |
Image recording | Average exposure time: 1.4 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 13936 |
Image scans | Width: 4096 / Height: 4096 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1366787 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75666 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 56.9 / Protocol: OTHER / Space: RECIPROCAL |