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- PDB-3j4j: Model of full-length T. thermophilus Translation Initiation Facto... -
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Basic information
Entry | Database: PDB / ID: 3j4j | ||||||
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Title | Model of full-length T. thermophilus Translation Initiation Factor 2 refined against its cryo-EM density from a 30S Initiation Complex map | ||||||
![]() | Translation initiation factor IF-2 | ||||||
![]() | TRANSLATION / IF2 / GTP-Binding Protein / fMet-tRNA binding / ribosome binding | ||||||
Function / homology | ![]() translation initiation factor activity / GTPase activity / GTP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.5 Å | ||||||
![]() | Simonetti, A. / Marzi, S. / Billas, I.M.L. / Tsai, A. / Fabbretti, A. / Myasnikov, A. / Roblin, P. / Vaiana, A.C. / Hazemann, I. / Eiler, D. ...Simonetti, A. / Marzi, S. / Billas, I.M.L. / Tsai, A. / Fabbretti, A. / Myasnikov, A. / Roblin, P. / Vaiana, A.C. / Hazemann, I. / Eiler, D. / Steitz, T.A. / Puglisi, J.D. / Gualerzi, C.O. / Klaholz, B.P. | ||||||
![]() | ![]() Title: Involvement of protein IF2 N domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor. Authors: Angelita Simonetti / Stefano Marzi / Isabelle M L Billas / Albert Tsai / Attilio Fabbretti / Alexander G Myasnikov / Pierre Roblin / Andrea C Vaiana / Isabelle Hazemann / Daniel Eiler / ...Authors: Angelita Simonetti / Stefano Marzi / Isabelle M L Billas / Albert Tsai / Attilio Fabbretti / Alexander G Myasnikov / Pierre Roblin / Andrea C Vaiana / Isabelle Hazemann / Daniel Eiler / Thomas A Steitz / Joseph D Puglisi / Claudio O Gualerzi / Bruno P Klaholz / ![]() Abstract: Translation initiation factor 2 (IF2) promotes 30S initiation complex (IC) formation and 50S subunit joining, which produces the 70S IC. The architecture of full-length IF2, determined by small angle ...Translation initiation factor 2 (IF2) promotes 30S initiation complex (IC) formation and 50S subunit joining, which produces the 70S IC. The architecture of full-length IF2, determined by small angle X-ray diffraction and cryo electron microscopy, reveals a more extended conformation of IF2 in solution and on the ribosome than in the crystal. The N-terminal domain is only partially visible in the 30S IC, but in the 70S IC, it stabilizes interactions between IF2 and the L7/L12 stalk of the 50S, and on its deletion, proper N-formyl-methionyl(fMet)-tRNA(fMet) positioning and efficient transpeptidation are affected. Accordingly, fast kinetics and single-molecule fluorescence data indicate that the N terminus promotes 70S IC formation by stabilizing the productive sampling of the 50S subunit during 30S IC joining. Together, our data highlight the dynamics of IF2-dependent ribosomal subunit joining and the role played by the N terminus of IF2 in this process. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 112.9 KB | Display | ![]() |
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PDB format | ![]() | 80.5 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2448MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 62494.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Buffer solution | Name: 10 mM HEPES, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 8 mM magnesium acetate, 1 mM DTT pH: 7.5 Details: 10 mM HEPES, pH 7.5, 70 mM NH4Cl, 30 mM KCl, 8 mM magnesium acetate, 1 mM DTT | ||||||||||||
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: Vitrification carried out in liquid ethane |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Oct 9, 2011 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: -3500 nm / Nominal defocus min: -1500 nm |
Specimen holder | Temperature: 70 K |
Image recording | Electron dose: 1.5 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||
3D reconstruction | Resolution: 11.5 Å / Num. of particles: 13000 / Nominal pixel size: 1.92 Å / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation coefficient Details: METHOD--cross-correlation gradient based REFINEMENT PROTOCOL--flexible fitting, dynamic elastic network | ||||||||||||||||
Refinement step | Cycle: LAST
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