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- EMDB-29822: Structure of the Escherichia coli 70S ribosome in complex with P-... -
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Open data
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Basic information
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Title | Structure of the Escherichia coli 70S ribosome in complex with P-site tRNAIle(LAU) bound to the cognate AUA codon (Structure IV) | |||||||||
![]() | Ribosome bound to P-site tRNAIle(LAU) and E-site tRNAIle(LAU) (Structure IV). | |||||||||
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![]() | lysidine 34 / cryo-EM / tRNA / RIBOSOME | |||||||||
Function / homology | ![]() negative regulation of cytoplasmic translational initiation / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of translational initiation / 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 / transcription antitermination ...negative regulation of cytoplasmic translational initiation / positive regulation of ribosome biogenesis / DnaA-L2 complex / negative regulation of translational initiation / 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 / transcription antitermination / translational initiation / regulation of cell growth / ribosomal large subunit assembly / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / large ribosomal subunit / 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 / mRNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Rybak MY / Gagnon MG | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of the ribosome bound to EF-Tu-isoleucine tRNA elucidate the mechanism of AUG avoidance. Authors: Mariia Yu Rybak / Matthieu G Gagnon / ![]() Abstract: The frequency of errors upon decoding of messenger RNA by the bacterial ribosome is low, with one misreading event per 1 × 10 codons. In the universal genetic code, the AUN codon box specifies ...The frequency of errors upon decoding of messenger RNA by the bacterial ribosome is low, with one misreading event per 1 × 10 codons. In the universal genetic code, the AUN codon box specifies two amino acids, isoleucine and methionine. In bacteria and archaea, decoding specificity of the AUA and AUG codons relies on the wobble avoidance strategy that requires modification of C34 in the anticodon loop of isoleucine transfer RNA (tRNA). Bacterial tRNA with 2-lysylcytidine (lysidine) at the wobble position deciphers AUA while avoiding AUG. Here we report cryo-electron microscopy structures of the Escherichia coli 70S ribosome complexed with elongation factor thermo unstable (EF-Tu) and isoleucine-tRNA in the process of decoding AUA and AUG. Lysidine in tRNA excludes AUG by promoting the formation of an unusual Hoogsteen purine-pyrimidine nucleobase geometry at the third position of the codon, weakening the interactions with the mRNA and destabilizing the EF-Tu ternary complex. Our findings elucidate the molecular mechanism by which tRNA specifically decodes AUA over AUG. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 254.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 77.1 KB 77.1 KB | Display Display | ![]() |
Images | ![]() | 219.5 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 15.4 KB | ||
Others | ![]() ![]() ![]() | 425 MB 476 MB 476 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8g7sMC ![]() 8g7pC ![]() 8g7qC ![]() 8g7rC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 | Ribosome bound to P-site tRNAIle(LAU) and E-site tRNAIle(LAU) (Structure IV). | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Ribosome bound to P-site tRNAIle(LAU) and E-site tRNAIle(LAU)...
File | emd_29822_additional_1.map | ||||||||||||
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Annotation | Ribosome bound to P-site tRNAIle(LAU) and E-site tRNAIle(LAU) (Structure IV). Sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Ribosome bound to P-site tRNAIle(LAU) and E-site tRNAIle(LAU)...
File | emd_29822_half_map_1.map | ||||||||||||
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Annotation | Ribosome bound to P-site tRNAIle(LAU) and E-site tRNAIle(LAU) (Structure IV). Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Ribosome bound to P-site tRNAIle(LAU) and E-site tRNAIle(LAU)...
File | emd_29822_half_map_2.map | ||||||||||||
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Annotation | Ribosome bound to P-site tRNAIle(LAU) and E-site tRNAIle(LAU) (Structure IV). Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Structure of the Escherichia coli 70S ribosome in complex with P-...
+Supramolecule #1: Structure of the Escherichia coli 70S ribosome in complex with P-...
+Macromolecule #1: 16S Ribosomal RNA
+Macromolecule #22: Isoleucine tRNA
+Macromolecule #23: I-F mRNA
+Macromolecule #24: 23S Ribosomal RNA
+Macromolecule #25: 5S Ribosomal RNA
+Macromolecule #2: 30S ribosomal protein S2
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: 30S ribosomal protein S8
+Macromolecule #9: 30S ribosomal protein S9
+Macromolecule #10: 30S ribosomal protein S10
+Macromolecule #11: 30S ribosomal protein S11
+Macromolecule #12: 30S ribosomal protein S12
+Macromolecule #13: 30S ribosomal protein S13
+Macromolecule #14: 30S ribosomal protein S14
+Macromolecule #15: 30S ribosomal protein S15
+Macromolecule #16: 30S ribosomal protein S16
+Macromolecule #17: 30S ribosomal protein S17
+Macromolecule #18: 30S ribosomal protein S18
+Macromolecule #19: 30S ribosomal protein S19
+Macromolecule #20: 30S ribosomal protein S20
+Macromolecule #21: 30S ribosomal protein S21
+Macromolecule #26: 50S ribosomal protein L2
+Macromolecule #27: 50S ribosomal protein L3
+Macromolecule #28: 50S ribosomal protein L4
+Macromolecule #29: 50S ribosomal protein L5
+Macromolecule #30: 50S ribosomal protein L6
+Macromolecule #31: 50S ribosomal protein L9
+Macromolecule #32: 50S ribosomal protein L13
+Macromolecule #33: 50S ribosomal protein L14
+Macromolecule #34: 50S ribosomal protein L15
+Macromolecule #35: 50S ribosomal protein L16
+Macromolecule #36: 50S ribosomal protein L17
+Macromolecule #37: 50S ribosomal protein L18
+Macromolecule #38: 50S ribosomal protein L19
+Macromolecule #39: 50S ribosomal protein L20
+Macromolecule #40: Ribosomal protein L21
+Macromolecule #41: 50S ribosomal protein L22
+Macromolecule #42: 50S ribosomal protein L23
+Macromolecule #43: 50S ribosomal protein L24
+Macromolecule #44: 50S ribosomal protein L25
+Macromolecule #45: 50S ribosomal protein L27
+Macromolecule #46: 50S ribosomal protein L28
+Macromolecule #47: 50S ribosomal protein L29
+Macromolecule #48: 50S ribosomal protein L30
+Macromolecule #49: 50S ribosomal protein L31
+Macromolecule #50: 50S ribosomal protein L32
+Macromolecule #51: 50S ribosomal protein L33
+Macromolecule #52: 50S ribosomal protein L34
+Macromolecule #53: 50S ribosomal protein L35
+Macromolecule #54: 50S ribosomal protein L36
+Macromolecule #55: MAGNESIUM ION
+Macromolecule #56: ISOLEUCINE
+Macromolecule #57: ZINC ION
+Macromolecule #58: 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: 7.4 |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 9711 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000 |
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 | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Software | Name: ![]() |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-8g7s: |