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- EMDB-27694: eEF1A(GDP)aa-tRNA stalled on the human 80S ribosome by ternatin-4 -
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Open data
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Basic information
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Title | eEF1A(GDP)aa-tRNA stalled on the human 80S ribosome by ternatin-4 | |||||||||
![]() | pixel calibrated | |||||||||
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![]() | Ribosome / eEF1A / ternatin / translation | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Rundlet EJ / Ferguson A / Juette MF / Carelli JD / Taunton J / Blanchard SC | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Didemnin B and ternatin-4 differentially inhibit conformational changes in eEF1A required for aminoacyl-tRNA accommodation into mammalian ribosomes. Authors: Manuel F Juette / Jordan D Carelli / Emily J Rundlet / Alan Brown / Sichen Shao / Angelica Ferguson / Michael R Wasserman / Mikael Holm / Jack Taunton / Scott C Blanchard / ![]() ![]() Abstract: Rapid and accurate mRNA translation requires efficient codon-dependent delivery of the correct aminoacyl-tRNA (aa-tRNA) to the ribosomal A site. In mammals, this fidelity-determining reaction is ...Rapid and accurate mRNA translation requires efficient codon-dependent delivery of the correct aminoacyl-tRNA (aa-tRNA) to the ribosomal A site. In mammals, this fidelity-determining reaction is facilitated by the GTPase elongation factor-1 alpha (eEF1A), which escorts aa-tRNA as an eEF1A(GTP)-aa-tRNA ternary complex into the ribosome. The structurally unrelated cyclic peptides didemnin B and ternatin-4 bind to the eEF1A(GTP)-aa-tRNA ternary complex and inhibit translation but have different effects on protein synthesis in vitro and in vivo. Here, we employ single-molecule fluorescence imaging and cryogenic electron microscopy to determine how these natural products inhibit translational elongation on mammalian ribosomes. By binding to a common site on eEF1A, didemnin B and ternatin-4 trap eEF1A in an intermediate state of aa-tRNA selection, preventing eEF1A release and aa-tRNA accommodation on the ribosome. We also show that didemnin B and ternatin-4 exhibit distinct effects on the dynamics of aa-tRNA selection that inform on observed disparities in their inhibition efficacies and physiological impacts. These integrated findings underscore the value of dynamics measurements in assessing the mechanism of small-molecule inhibition and highlight potential of single-molecule methods to reveal how distinct natural products differentially impact the human translation mechanism. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 194.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.2 KB 19.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 143.6 KB | ||
Filedesc metadata | ![]() | 4.5 KB | ||
Others | ![]() ![]() ![]() | 52.9 MB 194.3 MB 194.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | pixel calibrated | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.085 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: RELION Postprocessed, b factor -30, lowpass 4, pixel calibrated
File | emd_27694_additional_1.map | ||||||||||||
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Annotation | RELION Postprocessed, b factor -30, lowpass 4, pixel calibrated | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: pixel calibrated
File | emd_27694_half_map_1.map | ||||||||||||
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Annotation | pixel calibrated | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: pixel calibrated
File | emd_27694_half_map_2.map | ||||||||||||
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Annotation | pixel calibrated | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : eEF1A(GDP)aa-tRNA stalled on the human 80S ribosome by ternatin-4
Entire | Name: eEF1A(GDP)aa-tRNA stalled on the human 80S ribosome by ternatin-4 |
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Components |
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-Supramolecule #1: eEF1A(GDP)aa-tRNA stalled on the human 80S ribosome by ternatin-4
Supramolecule | Name: eEF1A(GDP)aa-tRNA stalled on the human 80S ribosome by ternatin-4 type: complex / ID: 1 / Parent: 0 |
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-Supramolecule #2: eEF1A(GDP)
Supramolecule | Name: eEF1A(GDP) / type: complex / ID: 2 / Parent: 1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Phe-tRNAPhe
Supramolecule | Name: Phe-tRNAPhe / type: complex / ID: 3 / Parent: 1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #4: Met-tRNAfMet
Supramolecule | Name: Met-tRNAfMet / type: complex / ID: 4 / Parent: 1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #5: 40S subunit
Supramolecule | Name: 40S subunit / type: complex / ID: 5 / Parent: 1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #6: 60S subunit
Supramolecule | Name: 60S subunit / type: complex / ID: 6 / Parent: 1 |
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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
Buffer | pH: 7.6 |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I |
Details | 20 uM ternatin-4 |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 2-50 / Number grids imaged: 3 / Number real images: 9401 / Average exposure time: 10.0 sec. / Average electron dose: 67.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.001 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |