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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8814 | |||||||||
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Title | 70S ribosome-EF-Tu H84A complex with GppNHp | |||||||||
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![]() | translation / GTPase / RIBOSOME | |||||||||
Function / homology | ![]() guanyl-nucleotide exchange factor complex / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / translational elongation / RNA folding ...guanyl-nucleotide exchange factor complex / negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / translational elongation / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translation elongation factor activity / four-way junction DNA binding / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / ribosome assembly / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / 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 / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / GTPase activity / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Fislage M / Brown Z | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-TuH84A. Authors: Marcus Fislage / Jingji Zhang / Zuben Patrick Brown / Chandra Sekhar Mandava / Suparna Sanyal / Måns Ehrenberg / Joachim Frank / ![]() ![]() Abstract: The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular ...The GTPase EF-Tu in ternary complex with GTP and aminoacyl-tRNA (aa-tRNA) promotes rapid and accurate delivery of cognate aa-tRNAs to the ribosomal A site. Here we used cryo-EM to study the molecular origins of the accuracy of ribosome-aided recognition of a cognate ternary complex and the accuracy-amplifying role of the monitoring bases A1492, A1493 and G530 of the 16S rRNA. We used the GTPase-deficient EF-Tu variant H84A with native GTP, rather than non-cleavable GTP analogues, to trap a near-cognate ternary complex in high-resolution ribosomal complexes of varying codon-recognition accuracy. We found that ribosome complexes trapped by GTPase-deficicent ternary complex due to the presence of EF-TuH84A or non-cleavable GTP analogues have very similar structures. We further discuss speed and accuracy of initial aa-tRNA selection in terms of conformational changes of aa-tRNA and stepwise activation of the monitoring bases at the decoding center of the ribosome. | |||||||||
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 | ![]() | 28.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 81.9 KB 81.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.8 KB | Display | ![]() |
Images | ![]() | 178.2 KB | ||
Masks | ![]() | 240.5 MB | ![]() | |
Filedesc metadata | ![]() | 15.5 KB | ||
Others | ![]() ![]() | 191.3 MB 191.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5we4MC ![]() 8813C ![]() 8815C ![]() 8826C ![]() 8828C ![]() 8829C ![]() 5wdtC ![]() 5we6C ![]() 5wf0C ![]() 5wfkC ![]() 5wfsC 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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Voxel size | X=Y=Z: 0.98 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: Half map 1
File | emd_8814_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_8814_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
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Density Histograms |
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Sample components
+Entire : 70S ribosome-EF-Tu (H84A) in complex with GppNHp
+Supramolecule #1: 70S ribosome-EF-Tu (H84A) in complex with GppNHp
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #34: 16S rRNA
+Macromolecule #55: tRNA-fMet
+Macromolecule #56: mRNA
+Macromolecule #57: Phe-tRNA-Phe
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L5
+Macromolecule #7: 50S ribosomal protein L6
+Macromolecule #8: 50S ribosomal protein L9
+Macromolecule #9: 50S ribosomal protein L11
+Macromolecule #10: 50S ribosomal protein L13
+Macromolecule #11: 50S ribosomal protein L14
+Macromolecule #12: 50S ribosomal protein L15
+Macromolecule #13: 50S ribosomal protein L16
+Macromolecule #14: 50S ribosomal protein L17
+Macromolecule #15: 50S ribosomal protein L18
+Macromolecule #16: 50S ribosomal protein L19
+Macromolecule #17: 50S ribosomal protein L20
+Macromolecule #18: 50S ribosomal protein L21
+Macromolecule #19: 50S ribosomal protein L22
+Macromolecule #20: 50S ribosomal protein L23
+Macromolecule #21: 50S ribosomal protein L24
+Macromolecule #22: 50S ribosomal protein L25
+Macromolecule #23: 50S ribosomal protein L27
+Macromolecule #24: 50S ribosomal protein L28
+Macromolecule #25: 50S ribosomal protein L29
+Macromolecule #26: 50S ribosomal protein L30
+Macromolecule #27: 50S ribosomal protein L32
+Macromolecule #28: 50S ribosomal protein L33
+Macromolecule #29: 50S ribosomal protein L34
+Macromolecule #30: 50S ribosomal protein L35
+Macromolecule #31: 50S ribosomal protein L36
+Macromolecule #32: 50S ribosomal protein L10
+Macromolecule #33: 50S ribosomal protein L31
+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 #58: Elongation factor Tu 2
+Macromolecule #59: MAGNESIUM ION
+Macromolecule #60: POTASSIUM ION
+Macromolecule #61: N-FORMYLMETHIONINE
+Macromolecule #62: PHENYLALANINE
+Macromolecule #63: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #64: 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 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.00933 kPa Details: grids were manually coated with gold and the carbon support was removed by glow discharge. gas mixture: 20% hydrogen/80% oxygen power: 15 W | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: 5 second blot time, no wait time. | |||||||||||||||||||||
Details | 300 nM 70S ribosome in final mixture |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2844 / Average exposure time: 0.2 sec. / Average electron dose: 67.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 30.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 51020 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: OTHER / Overall B value: 84 |
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Output model | ![]() PDB-5we4: |