|Entry||Database: PDB / ID: 3izy|
|Title||Mammalian mitochondrial translation initiation factor 2|
|Keywords||RNA / RIBOSOMAL PROTEIN / translation initiation factor 2 / IF2 / E coli|
|Specimen source||Bos taurus / mammal / cow / ウシ /|
|Method||Electron microscopy (10.8 Å resolution / Particle / Single particle)|
|Authors||Yassin, A.S. / Haque, E. / Datta, P.P. / Elmore, K. / Banavali, N.K. / Spremulli, L.L. / Agrawal, R.K.|
|Citation||Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 3918-3923|
Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 3918-3923 Yorodumi Papers
SummaryFull reportAbout validation report
|Date||Deposition: Jan 19, 2011 / Release: Mar 23, 2011|
Downloads & links
P: Translation initiation factor IF-2, mitochondrial
|#1: RNA chain|
Mass: 24518.570 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / mammal / ウシ /
Mass: 59602.250 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / mammal / ウシ / / References: UniProt: P46198
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Mammalian mitochondrial translation initiation factor 2 interaction with tRNA|
|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
Model: Tecnai F20 / Image courtesy: FEI Company
|Microscopy||Microscope 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 / Calibrated magnification: 50760|
|Image recording||Film or detector model: KODAK SO-163 FILM|
|EM software||Name: SPIDER / Category: RECONSTRUCTION|
|CTF correction||Details: Every Micrograph|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Method: Back Projection / Resolution: 10.8 Å / Number of particles: 121742 / Actual pixel size: 2.76 / Symmetry type: POINT|
|Number of atoms included #LAST||Protein: 4180 / Nucleic acid: 1622 / Ligand: 0 / Solvent: 0 / Total: 5802|
-Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
- Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi