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- EMDB-1854: An insertion domain within mammalian mitochondrial translation in... -

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Basic information

Entry
Database: EMDB / ID: EMD-1854
TitleAn insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1
Map dataE.coli 70S and mammalian mitochondrial IF2
Sample
  • Sample: E. coli 70S ribosome in complex with a mammalian mitochondrial translation initiation factor 2 and initiator transfer RNA
  • Complex: E. coli (MRE600) 70S ribosome
  • Protein or peptide: Bos taurus mitochondrial translation initiation factor 2
  • RNA: initiator fMet-transfer RNA
KeywordsE.coli 70S / mammalian mitochondrial IF2 translation initiation factor 2
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L14P, bacterial-type / Ribosomal protein L14P, conserved site / Ribosomal protein L14 signature. / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e
Similarity search - Domain/homology
Large ribosomal subunit protein uL14
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.8 Å
AuthorsYassin AS / Haque E / Datta PP / Elmore K / Banavali NK / Spremulli LL / Agrawal RK
CitationJournal: 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
DepositionJan 5, 2011-
Header (metadata) releaseFeb 18, 2011-
Map releaseMar 11, 2011-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 60
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 60
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3izz
  • Surface level: 60
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3izz
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-1854.tif

Downloads & links

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Map

FileDownload / File: emd_1854.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE.coli 70S and mammalian mitochondrial IF2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.76 Å/pix.
x 130 pix.
= 358.8 Å		2.76 Å/pix.
x 130 pix.
= 358.8 Å		2.76 Å/pix.
x 130 pix.
= 358.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 60.0 / Movie #1: 60
Minimum - Maximum-90.403499999999994 - 262.88900000000001
Average (Standard dev.)6.19491 (±29.836500000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-65-65-65
Dimensions130130130
Spacing130130130
CellA=B=C: 358.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z130130130
origin x/y/z-0.000-0.000-0.000
length x/y/z358.800358.800358.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-90.403262.8896.195

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Supplemental data

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Sample components

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Entire : E. coli 70S ribosome in complex with a mammalian mitochondrial tr...

EntireName: E. coli 70S ribosome in complex with a mammalian mitochondrial translation initiation factor 2 and initiator transfer RNA
Components
  • Sample: E. coli 70S ribosome in complex with a mammalian mitochondrial translation initiation factor 2 and initiator transfer RNA
  • Complex: E. coli (MRE600) 70S ribosome
  • Protein or peptide: Bos taurus mitochondrial translation initiation factor 2
  • RNA: initiator fMet-transfer RNA

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Supramolecule #1000: E. coli 70S ribosome in complex with a mammalian mitochondrial tr...

SupramoleculeName: 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
Molecular weightTheoretical: 2.5 MDa

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Supramolecule #1: E. coli (MRE600) 70S ribosome

SupramoleculeName: E. coli (MRE600) 70S ribosome / type: complex / ID: 1 / Name.synonym: Bacterial ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S, SSU 30S
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MRE600

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Macromolecule #1: Bos taurus mitochondrial translation initiation factor 2

MacromoleculeName: Bos taurus mitochondrial translation initiation factor 2
type: protein_or_peptide / ID: 1 / Name.synonym: mitochondrial translation IF2 / Recombinant expression: No
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine

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Macromolecule #2: initiator fMet-transfer RNA

MacromoleculeName: initiator fMet-transfer RNA / type: rna / ID: 2 / Name.synonym: fMet-tRNA / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferDetails: 0.5 mM GDPNP, 50mM Tris-HCl pH 7.6, 5mM MgCl2, 80mM KCl, 1mM dithiothreitol
GridDetails: 300 mesh copper
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 4.5 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingDigitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 392
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50760 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 50000
Sample stageSpecimen holder: Cryo / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each Micrograph
Final reconstructionApplied 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 classificationNumber classes: 43

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