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- EMDB-1854: An insertion domain within mammalian mitochondrial translation in... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1854 | |||||||||
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Title | An insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1 | |||||||||
![]() | E.coli 70S and mammalian mitochondrial IF2 | |||||||||
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![]() | E.coli 70S / mammalian mitochondrial IF2 translation initiation factor 2 | |||||||||
Function / homology | ![]() large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.8 Å | |||||||||
![]() | Yassin AS / Haque E / Datta PP / Elmore K / Banavali NK / Spremulli LL / Agrawal RK | |||||||||
![]() | ![]() Title: Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1. Authors: Aymen S Yassin / Md Emdadul Haque / Partha P Datta / Kevin Elmore / Nilesh K Banavali / Linda L Spremulli / Rajendra K Agrawal / ![]() Abstract: Mitochondria have their own translational machineries for the synthesis of thirteen polypeptide chains that are components of the complexes that participate in the process of oxidative ...Mitochondria have their own translational machineries for the synthesis of thirteen polypeptide chains that are components of the complexes that participate in the process of oxidative phosphorylation (or ATP generation). Translation initiation in mammalian mitochondria requires two initiation factors, IF2(mt) and IF3(mt), instead of the three that are present in eubacteria. The mammalian IF2(mt) possesses a unique 37 amino acid insertion domain, which is known to be important for the formation of the translation initiation complex. We have obtained a three-dimensional cryoelectron microscopic map of the mammalian IF2(mt) in complex with initiator fMet-tRNA(iMet) and the eubacterial ribosome. We find that the 37 amino acid insertion domain interacts with the same binding site on the ribosome that would be occupied by the eubacterial initiation factor IF1, which is absent in mitochondria. Our finding suggests that the insertion domain of IF2(mt) mimics the function of eubacterial IF1, by blocking the ribosomal aminoacyl-tRNA binding site (A site) at the initiation step. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.5 KB 9.5 KB | Display Display | ![]() |
Images | ![]() | 258.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3izzMC ![]() 1855C ![]() 3izyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | E.coli 70S and mammalian mitochondrial IF2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.76 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : E. coli 70S ribosome in complex with a mammalian mitochondrial tr...
Entire | Name: E. coli 70S ribosome in complex with a mammalian mitochondrial translation initiation factor 2 and initiator transfer RNA |
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Components |
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-Supramolecule #1000: E. coli 70S ribosome in complex with a mammalian mitochondrial tr...
Supramolecule | Name: E. coli 70S ribosome in complex with a mammalian mitochondrial translation initiation factor 2 and initiator transfer RNA type: sample / ID: 1000 / Number unique components: 3 |
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Molecular weight | Theoretical: 2.5 MDa |
-Supramolecule #1: E. coli (MRE600) 70S ribosome
Supramolecule | Name: E. coli (MRE600) 70S ribosome / type: complex / ID: 1 / Name.synonym: Bacterial ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S, SSU 30S |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Bos taurus mitochondrial translation initiation factor 2
Macromolecule | Name: Bos taurus mitochondrial translation initiation factor 2 type: protein_or_peptide / ID: 1 / Name.synonym: mitochondrial translation IF2 / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #2: initiator fMet-transfer RNA
Macromolecule | Name: initiator fMet-transfer RNA / type: rna / ID: 2 / Name.synonym: fMet-tRNA / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | Details: 0.5 mM GDPNP, 50mM Tris-HCl pH 7.6, 5mM MgCl2, 80mM KCl, 1mM dithiothreitol |
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Grid | Details: 300 mesh copper |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 4.5 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 392 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 50760 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000 |
Sample stage | Specimen holder: Cryo / Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Each Micrograph |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 121742 |
Final two d classification | Number classes: 43 |