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Basic information

Entry
Database: PDB / ID: 3izz
TitleModels for ribosome components that are nearest neighbors to the bovine mitochondrial initiation factor2 bound to the E. Coli ribosome
Components
  • Helix 18 (Small Subunit)
  • Helix 44 (Small Subunit)
  • Helix 5, 14, 15 (Small Subunit)
  • Helix 69, 71, 89, 92, 95 (Large Subunit)
  • Protein L14 (Large Subunit)
  • Protein S12 (Small Subunit)
KeywordsRNA / RIBOSOMAL PROTEIN / 70S
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / 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
RNA / RNA (> 10) / RNA (> 100) / Large ribosomal subunit protein uL14
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.8 Å
AuthorsYassin, A.S. / Haque, E. / Datta, P.P. / Elmore, K. / Banavali, N.K. / Spremulli, L.L. / Agrawal, R.K.
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 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Helix 5, 14, 15 (Small Subunit)
D: Helix 18 (Small Subunit)
E: Helix 44 (Small Subunit)
F: Protein S12 (Small Subunit)
B: Helix 69, 71, 89, 92, 95 (Large Subunit)
G: Protein L14 (Large Subunit)


Theoretical massNumber of molelcules
Total (without water)136,1256
Polymers136,1256
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 4 types, 4 molecules ADEB

#1: RNA chain Helix 5, 14, 15 (Small Subunit) /


Mass: 19027.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: RNA chain Helix 18 (Small Subunit)


Mass: 19467.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#3: RNA chain Helix 44 (Small Subunit)


Mass: 32453.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#5: RNA chain Helix 69, 71, 89, 92, 95 (Large Subunit) /


Mass: 38051.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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Protein , 2 types, 2 molecules FG

#4: Protein Protein S12 (Small Subunit)


Mass: 13804.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#6: Protein Protein L14 (Large Subunit)


Mass: 13320.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ADY3*PLUS

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Details

Sequence detailsCHAIN A IS MADE UP OF THREE HELICES (5,14, AND 15) OF SMALL SUBUNIT RNA AND CHAIN B IS COMPOSED OF ...CHAIN A IS MADE UP OF THREE HELICES (5,14, AND 15) OF SMALL SUBUNIT RNA AND CHAIN B IS COMPOSED OF HELICES 69, 71, 89, 92, AND 95 OF LARGE SUBUNIT RIBOSOME.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E. coli 70S / Type: RIBOSOME
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: Vitrobot

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Electron microscopy imaging

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

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: Every micrograph
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Back Projection / Resolution: 10.8 Å / Num. of particles: 121742 / Actual pixel size: 2.76 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 7218 0 0 9118

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