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- EMDB-1798: tRNA translocation on the 70S ribosome: the pre-translocational t... -
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Basic information
Entry | Database: EMDB / ID: EMD-1798 | |||||||||
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Title | tRNA translocation on the 70S ribosome: the pre-translocational translocation intermediate TI(PRE) | |||||||||
![]() | Cryo-EM map of the ribosomal 70S-tRNA-EFG-GDP-FA complex in the TI(PRE) state | |||||||||
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![]() | translation / ribosome / elongation cycle / tRNA translocation | |||||||||
Function / homology | ![]() ribosome disassembly / translation elongation factor activity / large ribosomal subunit / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity ...ribosome disassembly / translation elongation factor activity / large ribosomal subunit / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / protein homodimerization activity / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.8 Å | |||||||||
![]() | Ratje AH / Loerke J / Mikolajka A / Bruenner M / Hildebrand PW / Starosta AL / Doenhoefer A / Connell SR / Fucini P / Mielke T ...Ratje AH / Loerke J / Mikolajka A / Bruenner M / Hildebrand PW / Starosta AL / Doenhoefer A / Connell SR / Fucini P / Mielke T / Whitford PC / Onuchic J / Yu Y / Sanbonmatsu KY / Hartmann RK / Penczek PA / Wilson DN / Spahn CMT | |||||||||
![]() | ![]() Title: Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Authors: Andreas H Ratje / Justus Loerke / Aleksandra Mikolajka / Matthias Brünner / Peter W Hildebrand / Agata L Starosta / Alexandra Dönhöfer / Sean R Connell / Paola Fucini / Thorsten Mielke / ...Authors: Andreas H Ratje / Justus Loerke / Aleksandra Mikolajka / Matthias Brünner / Peter W Hildebrand / Agata L Starosta / Alexandra Dönhöfer / Sean R Connell / Paola Fucini / Thorsten Mielke / Paul C Whitford / José N Onuchic / Yanan Yu / Karissa Y Sanbonmatsu / Roland K Hartmann / Pawel A Penczek / Daniel N Wilson / Christian M T Spahn / ![]() Abstract: The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and ...The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and translocation of the tRNAs through the ribosome to reopen the A site. The translocation reaction is catalysed by elongation factor G (EF-G) in a GTP-dependent manner. Despite the availability of structures of various EF-G-ribosome complexes, the precise mechanism by which tRNAs move through the ribosome still remains unclear. Here we use multiparticle cryoelectron microscopy analysis to resolve two previously unseen subpopulations within Thermus thermophilus EF-G-ribosome complexes at subnanometre resolution, one of them with a partly translocated tRNA. Comparison of these substates reveals that translocation of tRNA on the 30S subunit parallels the swivelling of the 30S head and is coupled to unratcheting of the 30S body. Because the tRNA maintains contact with the peptidyl-tRNA-binding site (P site) on the 30S head and simultaneously establishes interaction with the exit site (E site) on the 30S platform, a novel intra-subunit 'pe/E' hybrid state is formed. This state is stabilized by domain IV of EF-G, which interacts with the swivelled 30S-head conformation. These findings provide direct structural and mechanistic insight into the 'missing link' in terms of tRNA intermediates involved in the universally conserved translocation process. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.4 KB 10.4 KB | Display Display | ![]() |
Images | ![]() | 768.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4v5mMC ![]() 1799C ![]() 4v5nC M: atomic model generated by this map C: citing same article ( |
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Similar 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 of the ribosomal 70S-tRNA-EFG-GDP-FA complex in the TI(PRE) state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : 70S-EFG-GDP-FA complex
Entire | Name: 70S-EFG-GDP-FA complex |
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Components |
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-Supramolecule #1000: 70S-EFG-GDP-FA complex
Supramolecule | Name: 70S-EFG-GDP-FA complex / type: sample / ID: 1000 / Oligomeric state: Monomer / Number unique components: 1 |
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-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Name.synonym: Thermus thermophilus 70S ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: Vitrobot (FEI) |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Average: 77 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 200,000 times magnification |
Details | Low-dose |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 4.7 µm / Number real images: 677 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 65520 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: Cartridge / Specimen holder model: GATAN HELIUM |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Defocus groups |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider |
-Atomic model buiding 1
Initial model | PDB ID: ![]() 2wrj |
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Software | Name: ![]() |
Details | Protocol: MDFIT |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
Output model | ![]() PDB-4v5m: |