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- EMDB-13458: Structure of the 70S ribosome with tRNAs in the classical pre-tra... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13458 | |||||||||
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Title | Structure of the 70S ribosome with tRNAs in the classical pre-translocation state and apramycin (C) | |||||||||
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![]() | EF-G / robosome / 70S / apramycin / translocation / RIBOSOME | |||||||||
Function / homology | ![]() stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation ...stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / 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 / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.35 Å | |||||||||
![]() | Petrychenko V / Peng BZ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural mechanism of GTPase-powered ribosome-tRNA movement. Authors: Valentyn Petrychenko / Bee-Zen Peng / Ana C de A P Schwarzer / Frank Peske / Marina V Rodnina / Niels Fischer / ![]() Abstract: GTPases are regulators of cell signaling acting as molecular switches. The translational GTPase EF-G stands out, as it uses GTP hydrolysis to generate force and promote the movement of the ribosome ...GTPases are regulators of cell signaling acting as molecular switches. The translational GTPase EF-G stands out, as it uses GTP hydrolysis to generate force and promote the movement of the ribosome along the mRNA. The key unresolved question is how GTP hydrolysis drives molecular movement. Here, we visualize the GTPase-powered step of ongoing translocation by time-resolved cryo-EM. EF-G in the active GDP-Pi form stabilizes the rotated conformation of ribosomal subunits and induces twisting of the sarcin-ricin loop of the 23 S rRNA. Refolding of the GTPase switch regions upon Pi release initiates a large-scale rigid-body rotation of EF-G pivoting around the sarcin-ricin loop that facilitates back rotation of the ribosomal subunits and forward swiveling of the head domain of the small subunit, ultimately driving tRNA forward movement. The findings demonstrate how a GTPase orchestrates spontaneous thermal fluctuations of a large RNA-protein complex into force-generating molecular movement. | |||||||||
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 | ![]() | 458.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 77.3 KB 77.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.2 KB | Display | ![]() |
Images | ![]() | 201.9 KB | ||
Masks | ![]() | 91.1 MB | ![]() | |
Filedesc metadata | ![]() | 15.2 KB | ||
Others | ![]() ![]() | 70.6 MB 70.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pjsMC ![]() 7pjtC ![]() 7pjuC ![]() 7pjvC ![]() 7pjwC ![]() 7pjxC ![]() 7pjyC ![]() 7pjzC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 987.5 Data #1: Motion-corrected, dose-weighted micrographs [micrographs - single frame] Data #2: Shiny particles of non-rotated ribosome particles (C state), obtained by Bayesian polishing in Relion 3.1 [picked particles - single frame - processed] Data #3: Shiny particles of rotated ribosome particles, obtained by Bayesian polishing in Relion 3.1 [picked particles - single frame - processed]) |
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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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Voxel size | X=Y=Z: 0.6525 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13458_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13458_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : E. coli ribosome complex 70S-Apr-EF-G-GDP-Pi-fMet-Phe-tRNAPhe-tRN...
+Supramolecule #1: E. coli ribosome complex 70S-Apr-EF-G-GDP-Pi-fMet-Phe-tRNAPhe-tRN...
+Macromolecule #1: 50S ribosomal protein L32
+Macromolecule #2: 50S ribosomal protein L33
+Macromolecule #3: 50S ribosomal protein L34
+Macromolecule #4: 50S ribosomal protein L35
+Macromolecule #5: 50S ribosomal protein L36
+Macromolecule #6: 50S ribosomal protein L10
+Macromolecule #7: 50S ribosomal protein L31
+Macromolecule #10: 50S ribosomal protein L2
+Macromolecule #11: 50S ribosomal protein L3
+Macromolecule #12: 50S ribosomal protein L4
+Macromolecule #13: 50S ribosomal protein L5
+Macromolecule #14: 50S ribosomal protein L6
+Macromolecule #15: 50S ribosomal protein L9
+Macromolecule #16: 50S ribosomal protein L11
+Macromolecule #17: 50S ribosomal protein L13
+Macromolecule #18: 50S ribosomal protein L14
+Macromolecule #19: 50S ribosomal protein L15
+Macromolecule #20: 50S ribosomal protein L16
+Macromolecule #21: 50S ribosomal protein L17
+Macromolecule #22: 50S ribosomal protein L18
+Macromolecule #23: 50S ribosomal protein L19
+Macromolecule #24: 50S ribosomal protein L20
+Macromolecule #25: 50S ribosomal protein L21
+Macromolecule #26: 50S ribosomal protein L22
+Macromolecule #27: 50S ribosomal protein L23
+Macromolecule #28: 50S ribosomal protein L24
+Macromolecule #29: 50S ribosomal protein L25
+Macromolecule #30: 50S ribosomal protein L27
+Macromolecule #31: 50S ribosomal protein L28
+Macromolecule #32: 50S ribosomal protein L29
+Macromolecule #33: 50S ribosomal protein L30
+Macromolecule #35: 30S ribosomal protein S2
+Macromolecule #36: 30S ribosomal protein S3
+Macromolecule #37: 30S ribosomal protein S4
+Macromolecule #38: 30S ribosomal protein S5
+Macromolecule #39: 30S ribosomal protein S6
+Macromolecule #40: 30S ribosomal protein S7
+Macromolecule #41: 30S ribosomal protein S8
+Macromolecule #42: 30S ribosomal protein S9
+Macromolecule #43: 30S ribosomal protein S10
+Macromolecule #44: 30S ribosomal protein S11
+Macromolecule #45: 30S ribosomal protein S12
+Macromolecule #46: 30S ribosomal protein S13
+Macromolecule #47: 30S ribosomal protein S14
+Macromolecule #48: 30S ribosomal protein S15
+Macromolecule #49: 30S ribosomal protein S16
+Macromolecule #50: 30S ribosomal protein S17
+Macromolecule #51: 30S ribosomal protein S18
+Macromolecule #52: 30S ribosomal protein S19
+Macromolecule #53: 30S ribosomal protein S20
+Macromolecule #54: 30S ribosomal protein S21
+Macromolecule #57: Dipeptide (FME-PHE)
+Macromolecule #8: 23S ribosomal RNA
+Macromolecule #9: 5S ribosomal RNA
+Macromolecule #34: 16S ribosomal RNA
+Macromolecule #55: P-site tRNA(fMet)
+Macromolecule #56: P-site fMet-Phe-tRNA(Phe)
+Macromolecule #58: mRNA
+Macromolecule #59: MAGNESIUM ION
+Macromolecule #60: ZINC ION
+Macromolecule #61: SODIUM ION
+Macromolecule #62: APRAMYCIN
+Macromolecule #63: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Details: 50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Manual blotting & plunge-freezing. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Details | Aberration corrections performed using Cs image corrector (CEOS company) |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 8221 / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated defocus max: 1.2 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Details | Instead of Chimera ChimeraX was used. | ||||||||
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: RSCC | ||||||||
Output model | ![]() PDB-7pjs: |