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- PDB-3izy: Mammalian mitochondrial translation initiation factor 2 -

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Database: PDB / ID: 3izy
TitleMammalian mitochondrial translation initiation factor 2
DescriptorPROTEIN/RNA Complex
KeywordsRNA / RIBOSOMAL PROTEIN / translation initiation factor 2 / IF2 / E coli
Specimen sourceBos taurus / mammal / cow / ウシ /
MethodElectron microscopy (10.8 Å resolution / Particle / Single particle)
AuthorsYassin, A.S. / Haque, E. / Datta, P.P. / Elmore, K. / Banavali, N.K. / Spremulli, L.L. / Agrawal, R.K.
CitationProc. Natl. Acad. Sci. U.S.A., 2011, 108, 3918-3923

Proc. Natl. Acad. Sci. U.S.A., 2011, 108, 3918-3923 Yorodumi Papers
Insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1.
Aymen S Yassin / Md Emdadul Haque / Partha P Datta / Kevin Elmore / Nilesh K Banavali / Linda L Spremulli / Rajendra K Agrawal

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 19, 2011 / Release: Mar 23, 2011
RevisionDateData content typeGroupProviderType
1.0Mar 23, 2011Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jan 21, 2015Structure modelStructure summary

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Deposited unit
N: tRNA-Phe
P: Translation initiation factor IF-2, mitochondrial

Theoretical massNumber of molelcules
Total (without water)84,1212

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


#1: RNA chaintRNA-Phe

Mass: 24518.570 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / mammal / ウシ /
#2: Polypeptide(L)Translation initiation factor IF-2, mitochondrial / IF-2(Mt) / IF-2Mt / IF2(mt)

Mass: 59602.250 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / mammal / ウシ / / References: UniProt: P46198

Cellular component

Molecular function

Biological process

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Mammalian mitochondrial translation initiation factor 2 interaction with tRNA
Buffer solutionDetails: 0.5mM GDPNP, 50mM Tris-HCl pH 7.6, 5mM MgCl2, 80mM KCl, 1mM dithiothreitol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Calibrated magnification: 50760
Image recordingFilm or detector model: KODAK SO-163 FILM


EM softwareName: SPIDER / Category: RECONSTRUCTION
CTF correctionDetails: Every Micrograph
SymmetryPoint symmetry: C1
3D reconstructionMethod: Back Projection / Resolution: 10.8 Å / Number of particles: 121742 / Actual pixel size: 2.76 / Symmetry type: POINT
Number of atoms included #LASTProtein: 4180 / Nucleic acid: 1622 / Ligand: 0 / Solvent: 0 / Total: 5802

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