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Yorodumi- EMDB-1855: An insertion domain within mammalian mitochondrial translation in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1855 | |||||||||
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Title | An insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1 | |||||||||
Map data | Mammalian mitochondrial translation initiation factor 2 | |||||||||
Sample |
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Keywords | E.coli 70S IF2 mammalian mitochondrial translation initiation factor 2 / cryo-EM | |||||||||
Function / homology | Function and homology information mitochondrial translational initiation / translation factor activity, RNA binding / ribosome disassembly / ribosomal small subunit binding / translation initiation factor activity / mitochondrial matrix / GTPase activity / GTP binding / mitochondrion / nucleoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.8 Å | |||||||||
Authors | Yassin AS / Haque E / Datta PP / Elmore K / Banavali NK / Spremulli LL / Agrawal RK | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2011 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1855.map.gz | 235.4 KB | EMDB map data format | |
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Header (meta data) | emd-1855-v30.xml emd-1855.xml | 8.3 KB 8.3 KB | Display Display | EMDB header |
Images | emd-1855.tif | 92.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1855 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1855 | HTTPS FTP |
-Validation report
Summary document | emd_1855_validation.pdf.gz | 283.9 KB | Display | EMDB validaton report |
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Full document | emd_1855_full_validation.pdf.gz | 283.5 KB | Display | |
Data in XML | emd_1855_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1855 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1855 | HTTPS FTP |
-Related structure data
Related structure data | 3izyMC 1854C 3izzC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1855.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mammalian mitochondrial translation initiation factor 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : mammalian mitochondrial translation initiation factor 2
Entire | Name: mammalian mitochondrial translation initiation factor 2 |
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Components |
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-Supramolecule #1000: mammalian mitochondrial translation initiation factor 2
Supramolecule | Name: mammalian mitochondrial translation initiation factor 2 type: sample / ID: 1000 Oligomeric state: Mammalian mitochondrial translation initiation factor 2 Number unique components: 1 |
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-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: Bos taurus (cattle) / synonym: bovine |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | Details: 0.5mM 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 |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Cryo / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-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 |