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- PDB-8g7p: Structure of the Escherichia coli 70S ribosome in complex with EF... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8g7p | |||||||||
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Title | Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and Ile-tRNAIle(LAU) bound to the cognate AUA codon (Structure I) | |||||||||
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![]() | RIBOSOME / Elongation factor Tu / lysidine 34 / cryo-EM / tRNA | |||||||||
Function / homology | ![]() negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / positive regulation of ribosome biogenesis / translation elongation factor activity / translational termination / DnaA-L2 complex / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity ...negative regulation of cytoplasmic translational initiation / guanosine tetraphosphate binding / stringent response / positive regulation of ribosome biogenesis / translation elongation factor activity / translational termination / 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 / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Rybak, M.Y. / Gagnon, M.G. | |||||||||
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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 29819MC ![]() 8g7qC ![]() 8g7rC ![]() 8g7sC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 6 types, 7 molecules awyxvAB
#1: RNA chain | Mass: 499873.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||
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#22: RNA chain | Mass: 24884.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Aminoacylated isoleucine-tRNA / Source: (gene. exp.) ![]() ![]() ![]() ![]() #23: RNA chain | | Mass: 24846.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Deacylated Initiator Methionyl-tRNA / Source: (gene. exp.) ![]() ![]() ![]() ![]() #24: RNA chain | | Mass: 8878.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic 27-nt M-I mRNA / Source: (synth.) ![]() #26: RNA chain | | Mass: 941811.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #27: RNA chain | | Mass: 38814.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-30S ribosomal protein ... , 20 types, 20 molecules bcdefghijklmnopqrstu
#2: Protein | Mass: 26795.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#3: Protein | Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 15211.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 17637.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 13871.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#13: Protein | Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein | Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#15: Protein | Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#17: Protein | Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#18: Protein | Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#19: Protein | Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#20: Protein | Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein | Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein , 2 types, 2 molecules zT
#25: Protein | Mass: 43152.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Elongation factor Tu / Source: (gene. exp.) ![]() ![]() Gene: tufA_2, tuf, tufA, tufA_1, tufA_3, tufA_4, tufB, tufB_1, tufB_2, A5U30_004581, A9X72_23960, AAS29_002155, AAS29_004093, ACN68_05365, AM464_13225, AT845_003992, AWP47_16755, B6R15_000408, BANRA_ ...Gene: tufA_2, tuf, tufA, tufA_1, tufA_3, tufA_4, tufB, tufB_1, tufB_2, A5U30_004581, A9X72_23960, AAS29_002155, AAS29_004093, ACN68_05365, AM464_13225, AT845_003992, AWP47_16755, B6R15_000408, BANRA_00548, BANRA_05052, BG944_004744, BGM66_002194, BJJ90_25160, BLM69_004391, BMT49_21045, BMT50_08130, BMT91_03325, BTQ06_27310, BvCmsKKP036_03588, BVL39_05405, BZL69_05770, C0P57_003010, C3F40_15505, C9E67_28700, CA593_06065, CCV12_004444, CDC27_21515, CO706_19465, CR538_24255, CR539_01630, CR628_004228, CV83915_02073, CY655_25255, D1H34_004550, D3Y67_20900, D9E49_24235, DAH19_24560, DAH21_23365, DAH22_22865, DAH27_25225, DAH28_23840, DAH32_23225, DAH33_24610, DAH34_21600, DAH37_22525, DAH38_23185, DAH40_23380, DAH41_23505, DAH42_24340, DAH43_24835, DAH45_24780, DAH46_24615, DAH47_25180, DAH48_24880, DAH49_24790, DNQ45_05140, DS732_01505, DU321_23465, E3N34_20940, E5P27_19115, E5P28_08865, E5P29_14360, EC95NR1_03445, EKI52_13985, EL79_4415, ELT25_22120, ELU85_23630, ELU98_01540, ELV02_23595, ELV12_15580, ExPECSC038_04335, FA849_13360, FA849_22895, FE584_21060, FE587_22575, FEL34_21300, FHO90_24295, FOI11_015750, FOI11_24390, FZN31_22945, FZU14_22815, G9448_13515, GAJ12_23515, GJ11_25160, H0O37_04690, H6Y26_004587, HV109_22460, HV146_01010, HV146_21790, HV209_21230, HVV39_13100, HVW04_13870, HVW43_15020, HVX31_01850, HVX31_19145, HVX32_01070, HVX32_19165, HVY77_24410, HVZ29_01065, HVZ29_19215, HVZ30_01935, HVZ30_19855, HVZ71_23905, HX136_23675, I6H00_17205, I6H01_14295, I6H02_15680, JE86ST02C_45170, JE86ST05C_45270, JFD_05085, JNP96_01240, NCTC10082_02089, NCTC10089_04881, NCTC10418_07157, NCTC10764_02980, NCTC10767_00724, NCTC10865_05903, NCTC11112_02273, NCTC11126_05444, NCTC11181_01973, NCTC11341_02766, NCTC12950_05222, NCTC13127_06172, NCTC13148_04399, NCTC13216_02099, NCTC4450_01743, NCTC7927_05257, NCTC7928_03622, NCTC8333_05566, NCTC8500_05333, NCTC8621_04880, NCTC8959_04056, NCTC8960_02348, NCTC9036_04657, NCTC9037_04790, NCTC9044_02296, NCTC9045_05550, NCTC9073_00863, NCTC9075_06435, NCTC9077_05944, NCTC9111_04963, NCTC9117_05912, NCTC9702_05647, NCTC9706_02011, NCTC9775_03134, NCTC9777_01126, RG28_25305, SAMEA3472044_04882, SAMEA3751407_05016, SAMEA3752557_04835, SAMEA3753106_04223, TUM18780_41760, WP4S18E07_42760 Plasmid: pET21a-EF-Tu / Production host: ![]() ![]() |
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#43: Protein | Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+50S ribosomal protein ... , 29 types, 29 molecules CDEFGHJLMNOPQRSUVWXYZ12345678
-Non-polymers , 6 types, 1599 molecules ![](data/chem/img/MG.gif)
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![](data/chem/img/ILE.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/ILE.gif)
![](data/chem/img/GCP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#58: Chemical | ChemComp-MG / #59: Chemical | #60: Chemical | #61: Chemical | ChemComp-GCP / | #62: Chemical | #63: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Structure of the Escherichia coli 70S ribosome in complex with EF-Tu and Ile-tRNAIle(LAU) bound to the cognate AUA codon (Structure I) Type: RIBOSOME / Entity ID: #1-#57 / Source: NATURAL |
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Molecular weight | Value: 2.6 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 295 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 96000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10381 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135882 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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