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Yorodumi- EMDB-35001: E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and t6A... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35001 | ||||||||||||||||||
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Title | E. coli 70S ribosome complexed with tRNA_Ile2 bearing L34 and t6A37 in classical state | ||||||||||||||||||
Map data | Before post-processing | ||||||||||||||||||
Sample |
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Keywords | tRNA modification / decoding / RIBOSOME | ||||||||||||||||||
Function / homology | Function and homology information negative regulation of cytoplasmic translational initiation / mRNA base-pairing translational repressor activity / 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 ...negative regulation of cytoplasmic translational initiation / mRNA base-pairing translational repressor activity / 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 / translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / positive regulation of RNA splicing / transcription elongation factor complex / response to reactive oxygen species / DNA endonuclease activity / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / regulation of translation / ribosome biogenesis / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / small ribosomal subunit / 5S rRNA binding / transferase activity / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli BW25113 (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.32 Å | ||||||||||||||||||
Authors | Akiyama N / Ishiguro K / Yokoyama T / Shirouzu M / Suzuki T | ||||||||||||||||||
Funding support | Japan, 5 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Structural insights into the decoding capability of isoleucine tRNAs with lysidine and agmatidine. Authors: Naho Akiyama / Kensuke Ishiguro / Takeshi Yokoyama / Kenjyo Miyauchi / Asuteka Nagao / Mikako Shirouzu / Tsutomu Suzuki / Abstract: The anticodon modifications of transfer RNAs (tRNAs) finetune the codon recognition on the ribosome for accurate translation. Bacteria and archaea utilize the modified cytidines, lysidine (L) and ...The anticodon modifications of transfer RNAs (tRNAs) finetune the codon recognition on the ribosome for accurate translation. Bacteria and archaea utilize the modified cytidines, lysidine (L) and agmatidine (agmC), respectively, in the anticodon of tRNA to decipher AUA codon. L and agmC contain long side chains with polar termini, but their functions remain elusive. Here we report the cryogenic electron microscopy structures of tRNAs recognizing the AUA codon on the ribosome. Both modifications interact with the third adenine of the codon via a unique C-A geometry. The side chains extend toward 3' direction of the mRNA, and the polar termini form hydrogen bonds with 2'-OH of the residue 3'-adjacent to the AUA codon. Biochemical analyses demonstrated that AUA decoding is facilitated by the additional interaction between the polar termini of the modified cytidines and 2'-OH of the fourth mRNA residue. We also visualized cyclic N-threonylcarbamoyladenosine (ctA), another tRNA modification, and revealed a molecular basis how ctA contributes to efficient decoding. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35001.map.gz | 531.9 MB | EMDB map data format | |
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Header (meta data) | emd-35001-v30.xml emd-35001.xml | 89 KB 89 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35001_fsc.xml | 18.6 KB | Display | FSC data file |
Images | emd_35001.png | 77.5 KB | ||
Filedesc metadata | emd-35001.cif.gz | 15.7 KB | ||
Others | emd_35001_additional_1.map.gz emd_35001_half_map_1.map.gz emd_35001_half_map_2.map.gz | 459.1 MB 461 MB 461 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35001 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35001 | HTTPS FTP |
-Related structure data
Related structure data | 8hspMC 8htzC 8hu1C 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_35001.map.gz / Format: CCP4 / Size: 567.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Before post-processing | ||||||||||||||||||||
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_35001_additional_1.map | ||||||||||||
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Annotation | Before post-processing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35001_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35001_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: A-, P- site tRNA
+Supramolecule #4: mRNA
+Macromolecule #1: 16S rRNA
+Macromolecule #22: 23S rRNA
+Macromolecule #23: 5S rRNA
+Macromolecule #53: P-site tRNA_Glu
+Macromolecule #54: mRNA
+Macromolecule #55: A-site tRNA_Ile2
+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
+Macromolecule #57: POTASSIUM 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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec. | |||||||||||||||
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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6914 / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |