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- EMDB-1173: Conformational transition of initiation factor 2 from the GTP- to... -
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Basic information
Entry | Database: EMDB / ID: EMD-1173 | |||||||||
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Title | Conformational transition of initiation factor 2 from the GTP- to GDP-bound state visualized on the ribosome. | |||||||||
![]() | cryo-EM map for T. thermophilus ribosomal complex with initiation factor IF2 in the GTP state | |||||||||
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Function / homology | Translation initiation factor IF-2, bacterial-like / translational initiation![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 11.0 Å | |||||||||
![]() | Myasnikov AG / Marzi S / Simonetti A / Giuliodori AM / Gualerzi CO / Yusupova G / Yusupov M / Klaholz BP | |||||||||
![]() | ![]() Title: Conformational transition of initiation factor 2 from the GTP- to GDP-bound state visualized on the ribosome. Authors: Alexander G Myasnikov / Stefano Marzi / Angelita Simonetti / Anna Maria Giuliodori / Claudio O Gualerzi / Gulnara Yusupova / Marat Yusupov / Bruno P Klaholz / ![]() Abstract: Initiation of protein synthesis is a universally conserved event that requires initiation factors IF1, IF2 and IF3 in prokaryotes. IF2 is a GTPase essential for binding initiator transfer RNA to the ...Initiation of protein synthesis is a universally conserved event that requires initiation factors IF1, IF2 and IF3 in prokaryotes. IF2 is a GTPase essential for binding initiator transfer RNA to the 30S ribosomal subunit and recruiting the 50S subunit into the 70S initiation complex. We present two cryo-EM structures of the assembled 70S initiation complex comprising mRNA, fMet-tRNA(fMet) and IF2 with either a non-hydrolyzable GTP analog or GDP. Transition from the GTP-bound to the GDP-bound state involves substantial conformational changes of IF2 and of the entire ribosome. In the GTP analog-bound state, IF2 interacts mostly with the 30S subunit and extends to the initiator tRNA in the peptidyl (P) site, whereas in the GDP-bound state IF2 steps back and adopts a 'ready-to-leave' conformation. Our data also provide insights into the molecular mechanism guiding release of IF1 and IF3. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.2 KB 12.2 KB | Display Display | ![]() |
Images | ![]() | 35.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | cryo-EM map for T. thermophilus ribosomal complex with initiation factor IF2 in the GTP state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Ribosome complex with initiation factor 2 in GDP state
Entire | Name: Ribosome complex with initiation factor 2 in GDP state |
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Components |
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-Supramolecule #1000: Ribosome complex with initiation factor 2 in GDP state
Supramolecule | Name: Ribosome complex with initiation factor 2 in GDP state type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 4 |
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Molecular weight | Theoretical: 2.5 MDa |
-Supramolecule #1: 70S
Supramolecule | Name: 70S / type: complex / ID: 1 / Name.synonym: 70S / Details: Thermus thermophilus 70S ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: messenger RNA
Macromolecule | Name: messenger RNA / type: rna / ID: 1 / Name.synonym: mRNA / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: GGCAAGGAGG UAAAAAUGAA AAAAAAA |
-Macromolecule #2: formyl-methionyl-RNA
Macromolecule | Name: formyl-methionyl-RNA / type: rna / ID: 2 / Name.synonym: fMet-tRNA / Classification: TRANSFER / Structure: SINGLE STRANDED / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
Sequence | String: CGCGGGGGGA GCAGCCUGGU AGCUCGUCGG GCUCAUAACC CGAAGGUCGU CGGUUCAAAU CCGGCCCCCG CAACCA |
-Macromolecule #3: initiation factor 2
Macromolecule | Name: initiation factor 2 / type: protein_or_peptide / ID: 3 / Name.synonym: IF2 / Details: Factor with GDP nucleotide / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | GO: translational initiation InterPro: Translation initiation factor IF-2, bacterial-like |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.5 Details: 20mM Tris-HCl (pH7.5) ,20mM MgCl2, 100mM KCl, 1mM DTT |
Staining | Type: NEGATIVE / Details: no staining, cryo-EM with holey carbon grids |
Grid | Details: 300 mesh Copper/Rhodium grid |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: home-made cryo-plunger / Method: Blot for 2 seconds before plunging |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 77 K |
Alignment procedure | Legacy - Astigmatism: lens astigmatism was corrected at 50,000 times magnification |
Date | Nov 17, 2004 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 3 µm / Number real images: 40 / Average electron dose: 10 e/Å2 / Details: Heidelberg Druckmaschinen / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Software | Name: program O |
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Details | Protocol: Rigid Body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |