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Yorodumi- EMDB-39581: E. coli 70S ribosome complexed with P.putida tRNAIle2 and A(F)4 mRNA -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39581 | ||||||||||||
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Title | E. coli 70S ribosome complexed with P.putida tRNAIle2 and A(F)4 mRNA | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | tRNA modification / decoding / RIBOSOME | ||||||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis ...negative regulation of cytoplasmic translational initiation / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / four-way junction DNA binding / 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 / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / cytosolic ribosome assembly / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / regulation of cell growth / translational initiation / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / transferase activity / small ribosomal subunit / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / molecular adaptor activity / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Escherichia coli (E. coli) / Pseudomonas putida NBRC 14164 (bacteria) / Escherichia coli BW25113 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.43 Å | ||||||||||||
Authors | Akiyama N / Ishiguro K / Shirouzu M / Suzuki T | ||||||||||||
Funding support | Japan, 3 items
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Citation | Journal: Nat Chem Biol / Year: 2024 Title: A tRNA modification with aminovaleramide facilitates AUA decoding in protein synthesis. Authors: Kenjyo Miyauchi / Satoshi Kimura / Naho Akiyama / Kazuki Inoue / Kensuke Ishiguro / Thien-Son Vu / Veerasak Srisuknimit / Kenta Koyama / Gosuke Hayashi / Akiko Soma / Asuteka Nagao / Mikako ...Authors: Kenjyo Miyauchi / Satoshi Kimura / Naho Akiyama / Kazuki Inoue / Kensuke Ishiguro / Thien-Son Vu / Veerasak Srisuknimit / Kenta Koyama / Gosuke Hayashi / Akiko Soma / Asuteka Nagao / Mikako Shirouzu / Akimitsu Okamoto / Matthew K Waldor / Tsutomu Suzuki / Abstract: Modified tRNA anticodons are critical for proper mRNA translation during protein synthesis. It is generally thought that almost all bacterial tRNAs use a modified cytidine-lysidine (L)-at the first ...Modified tRNA anticodons are critical for proper mRNA translation during protein synthesis. It is generally thought that almost all bacterial tRNAs use a modified cytidine-lysidine (L)-at the first position (34) of the anticodon to decipher the AUA codon as isoleucine (Ile). Here we report that tRNAs from plant organelles and a subset of bacteria contain a new cytidine derivative, designated 2-aminovaleramididine (avaC). Like L34, avaC34 governs both Ile-charging ability and AUA decoding. Cryo-electron microscopy structural analyses revealed molecular details of codon recognition by avaC34 with a specific interaction between its terminal amide group and an mRNA residue 3'-adjacent to the AUA codon. These findings reveal the evolutionary variation of an essential tRNA modification and demonstrate the molecular basis of AUA decoding mediated by a unique tRNA modification. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39581.map.gz | 530.9 MB | EMDB map data format | |
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Header (meta data) | emd-39581-v30.xml emd-39581.xml | 86.1 KB 86.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_39581_fsc.xml | 18.7 KB | Display | FSC data file |
Images | emd_39581.png | 96.3 KB | ||
Filedesc metadata | emd-39581.cif.gz | 15.6 KB | ||
Others | emd_39581_additional_1.map.gz emd_39581_half_map_1.map.gz emd_39581_half_map_2.map.gz | 457.1 MB 459.4 MB 459.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39581 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39581 | HTTPS FTP |
-Validation report
Summary document | emd_39581_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_39581_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_39581_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | emd_39581_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39581 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39581 | HTTPS FTP |
-Related structure data
Related structure data | 8yusMC 8yuoC 8yupC 8yuqC 8yurC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_39581.map.gz / Format: CCP4 / Size: 567.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8285 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Before post-processing
File | emd_39581_additional_1.map | ||||||||||||
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Annotation | Before post-processing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_39581_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_39581_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : The complex of E. coli 70S ribosome with mRNA and A-, P- site tRNA
+Supramolecule #1: The complex of E. coli 70S ribosome with mRNA and A-, P- site tRNA
+Supramolecule #2: E. coli 70S ribosome
+Supramolecule #3: mRNA
+Supramolecule #4: A-site tRNAIle2
+Supramolecule #5: P-site tRNAGlu
+Macromolecule #1: 16S rRNA
+Macromolecule #22: 23S rRNA
+Macromolecule #23: 5S rRNA
+Macromolecule #53: P-site tRNAGlu
+Macromolecule #54: mRNA
+Macromolecule #55: A-site tRNAIle2
+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, fully modified isoform
+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 #24: 50S ribosomal protein L2
+Macromolecule #25: 50S ribosomal protein L3
+Macromolecule #26: 50S ribosomal protein L4
+Macromolecule #27: 50S ribosomal protein L5
+Macromolecule #28: 50S ribosomal protein L6
+Macromolecule #29: 50S ribosomal protein L9
+Macromolecule #30: 50S ribosomal protein L13
+Macromolecule #31: 50S ribosomal protein L14
+Macromolecule #32: 50S ribosomal protein L15
+Macromolecule #33: 50S ribosomal protein L16
+Macromolecule #34: 50S ribosomal protein L17
+Macromolecule #35: 50S ribosomal protein L18
+Macromolecule #36: 50S ribosomal protein L19
+Macromolecule #37: 50S ribosomal protein L20
+Macromolecule #38: 50S ribosomal protein L21
+Macromolecule #39: 50S ribosomal protein L22
+Macromolecule #40: 50S ribosomal protein L23
+Macromolecule #41: 50S ribosomal protein L24
+Macromolecule #42: 50S ribosomal protein L25
+Macromolecule #43: 50S ribosomal protein L27
+Macromolecule #44: 50S ribosomal protein L28
+Macromolecule #45: 50S ribosomal protein L29
+Macromolecule #46: 50S ribosomal protein L30
+Macromolecule #47: 50S ribosomal protein L32
+Macromolecule #48: 50S ribosomal protein L33
+Macromolecule #49: 50S ribosomal protein L34
+Macromolecule #50: 50S ribosomal protein L35
+Macromolecule #51: 50S ribosomal protein L36
+Macromolecule #52: 50S ribosomal protein L31
+Macromolecule #56: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Component:
Details: The Buffer pH was adjusted to 7.6 using KOH. | |||||||||||||||
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | 100nM ribosomes were incubated with 500nM tRNAs and mRNA |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7206 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |