+Open data
-Basic information
Entry | Database: PDB / ID: 3izy | ||||||
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Title | Mammalian mitochondrial translation initiation factor 2 | ||||||
Components |
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Keywords | RNA / RIBOSOMAL PROTEIN / translation initiation factor 2 / IF2 / E coli | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.8 Å | ||||||
Authors | Yassin, A.S. / Haque, E. / Datta, P.P. / Elmore, K. / Banavali, N.K. / Spremulli, L.L. / Agrawal, R.K. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3izy.cif.gz | 142 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3izy.ent.gz | 102.3 KB | Display | PDB format |
PDBx/mmJSON format | 3izy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3izy_validation.pdf.gz | 636.8 KB | Display | wwPDB validaton report |
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Full document | 3izy_full_validation.pdf.gz | 667.6 KB | Display | |
Data in XML | 3izy_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 3izy_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/3izy ftp://data.pdbj.org/pub/pdb/validation_reports/iz/3izy | HTTPS FTP |
-Related structure data
Related structure data | 1855MC 1854C 3izzC 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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-Components
#1: RNA chain | Mass: 24518.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) |
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#2: Protein | Mass: 59602.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P46198 |
-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 factor 2 interaction with tRNA Type: RIBOSOME |
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Buffer solution | Details: 0.5mM GDPNP, 50mM Tris-HCl pH 7.6, 5mM MgCl2, 80mM KCl, 1mM dithiothreitol |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50760 X |
Image recording | Film or detector model: KODAK SO-163 FILM |
-Processing
EM software | Name: SPIDER / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: Every Micrograph | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: Back Projection / Resolution: 10.8 Å / Num. of particles: 121742 / Actual pixel size: 2.76 Å / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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