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Yorodumi- PDB-6gaw: Unique features of mammalian mitochondrial translation initiation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gaw | ||||||||||||
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Title | Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM. This file contains the complete 55S ribosome. | ||||||||||||
Components |
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Keywords | RIBOSOME / translation initiation / initiation factor IF2 / mitochondria / membrane targeting | ||||||||||||
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 initiation / translation factor activity, RNA binding / mitochondrial transcription ...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 initiation / translation factor activity, RNA binding / mitochondrial transcription / mitochondrial ribosome assembly / mitochondrial translational elongation / mitochondrial translational termination / ribonuclease III activity / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation initiation / Mitochondrial protein degradation / ribosome disassembly / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / regulation of translational initiation / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / organelle membrane / positive regulation of proteolysis / ribosomal small subunit binding / RNA processing / translation initiation factor activity / rescue of stalled ribosome / double-stranded RNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / nuclear membrane / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / cell cycle / protein domain specific binding / nucleotide binding / GTPase activity / mRNA binding / apoptotic process / synapse / nucleolus / GTP binding / positive regulation of DNA-templated transcription / 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: 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 | 6gaw.cif.gz | 4.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6gaw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6gaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gaw_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 6gaw_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6gaw_validation.xml.gz | 373.6 KB | Display | |
Data in CIF | 6gaw_validation.cif.gz | 631.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/6gaw ftp://data.pdbj.org/pub/pdb/validation_reports/ga/6gaw | HTTPS FTP |
-Related structure data
Related structure data | 4368MC 4369C 4370C 6gazC 6gb2C 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 ... , 35 types, 41 molecules CLDLELFLGLHLBLB0B1B2B7B8BFBIBJBKBSBTBUBVBaBbBcBeBjBkBnBtBxAB...
+Protein , 29 types, 29 molecules B3B5B6B9BCBEBOBWBXBfBgBiBmBpBqBuBvBwAOAPAQAUAeAgAhAiAmAnAo
-39S ribosomal protein ... , 11 types, 11 molecules B4BDBNBPBQBRBYBdBhBlBo
#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 |
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#15: Protein | Mass: 33270.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RRN2 |
#21: Protein | Mass: 20633.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GP19 |
#23: Protein | Mass: 33481.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RSH0 |
#24: Protein | Mass: 28680.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RI89 |
#25: Protein | Mass: 19268.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RMQ4 |
#32: Protein | Mass: 24893.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: F1RHJ1 |
#36: Protein | Mass: 24075.658 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZP98 |
#40: Protein | Mass: 37527.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SR64 |
#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 |
#47: Protein | Mass: 13813.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S9B7 |
-RNA chain , 5 types, 5 molecules BABBAAAVAX
#12: RNA chain | Mass: 504852.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / 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 / Details: CCA end is added post-transcriptionally. / Source: (natural) Sus scrofa (pig) / Organ: liver / References: GenBank: 76262549 |
#56: RNA chain | Mass: 308989.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: GenBank: 11055671 |
#72: RNA chain | Mass: 22664.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1390216722 |
#73: RNA chain | Mass: 63946.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 1388777935 |
-Unassigned secondary structure ... , 2 types, 2 molecules BzAZ
#55: Protein | Mass: 5846.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Unassigned secondary structure elements built as poly-alanine. Source: (natural) Sus scrofa (pig) |
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#74: Protein/peptide | Mass: 1297.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Unassigned secondary structure elements built as poly-alanine. Source: (natural) Sus scrofa (pig) / Organ: liver |
-28S ribosomal protein ... , 7 types, 7 molecules AIAKAbAfAjAkAp
#62: Protein | Mass: 45604.570 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) / References: UniProt: I3LU08 |
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#64: Protein | Mass: 20841.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZJJ6 |
#76: Protein | Mass: 21666.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AEW3 |
#80: Protein | Mass: 21014.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: liver / References: UniProt: A0A0M3KL56 |
#84: Protein | Mass: 25843.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RG19 |
#85: Protein | Mass: 37104.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SG95 |
#89: Protein | Mass: 29220.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q767K8 |
-Non-polymers , 9 types, 346 molecules
#90: Chemical | ChemComp-MG / #91: Chemical | ChemComp-ZN / #92: Chemical | #93: Chemical | #94: Chemical | ChemComp-GSP / | #95: Chemical | ChemComp-NA / | #96: Chemical | ChemComp-FME / | #97: Chemical | ChemComp-GTP / | #98: 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 | Name: mammalian mitochondrial translation initiation complex Type: RIBOSOME / Entity ID: #1-#89 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 2.85 MDa / Experimental value: NO |
Source (natural) | Organism: sus sucorfa (pig) |
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 FIELD |
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 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139206 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 66.8 / Protocol: OTHER / Space: RECIPROCAL |