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Yorodumi- EMDB-12035: E. coli 70S containing suppressor tRNA in the A-site stabilized b... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12035 | |||||||||
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Title | E. coli 70S containing suppressor tRNA in the A-site stabilized by a Negamycin analogue and P-site tRNA-nascent chain. | |||||||||
Map data | Post Process map | |||||||||
Sample |
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Keywords | Cryo-EM / 70S / P-site tRNA / E-site tRNA / Erythromycin / N6-(3aminopropyl)-negamycin / Antibiotics / 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 / four-way junction DNA binding / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / negative regulation of translational 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 / regulation of DNA-templated transcription elongation / cytosolic ribosome assembly / DNA endonuclease activity / response to reactive oxygen species / transcription antitermination / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / large ribosomal subunit / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / 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 K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Albers S / Beckert B | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Harnessing evolutionarily flexibility in tRNAs to maximize nonsense suppression activities Authors: Albers S / Beckert B / Wilson ND / Ignatova Z | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12035.map.gz | 31.9 MB | EMDB map data format | |
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Header (meta data) | emd-12035-v30.xml emd-12035.xml | 89.3 KB 89.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12035_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_12035.png | 278.5 KB | ||
Filedesc metadata | emd-12035.cif.gz | 14.4 KB | ||
Others | emd_12035_additional_1.map.gz emd_12035_additional_2.map.gz emd_12035_additional_3.map.gz emd_12035_additional_4.map.gz emd_12035_half_map_1.map.gz emd_12035_half_map_2.map.gz | 32.1 MB 32 MB 31.9 MB 139.7 MB 140.3 MB 140.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12035 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12035 | HTTPS FTP |
-Validation report
Summary document | emd_12035_validation.pdf.gz | 1005.7 KB | Display | EMDB validaton report |
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Full document | emd_12035_full_validation.pdf.gz | 1005.3 KB | Display | |
Data in XML | emd_12035_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | emd_12035_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12035 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12035 | HTTPS FTP |
-Related structure data
Related structure data | 7b5kMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12035.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Post Process map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.96 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Multi body LSU
File | emd_12035_additional_1.map | ||||||||||||
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Annotation | Multi body LSU | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Multi body SSU-body
File | emd_12035_additional_2.map | ||||||||||||
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Annotation | Multi body SSU-body | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Multi body SSU-head
File | emd_12035_additional_3.map | ||||||||||||
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Annotation | Multi body SSU-head | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: relion final 3D refine
File | emd_12035_additional_4.map | ||||||||||||
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Annotation | relion final 3D refine | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_12035_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_12035_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 70S ribosome with A,P,E-site tRNA
+Supramolecule #1: 70S ribosome with A,P,E-site tRNA
+Supramolecule #2: 70S ribosome with A,P,E-site tRNA
+Supramolecule #3: mRNA
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #32: 16S rRNA
+Macromolecule #54: P-site Isoleucine tRNA (77-MER)
+Macromolecule #55: atRNA synthetic Stop tRNA (76-MER)
+Macromolecule #56: E-site val tRNA (76-MER)
+Macromolecule #57: mRNA
+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 L13
+Macromolecule #10: 50S ribosomal protein L14
+Macromolecule #11: 50S ribosomal protein L15
+Macromolecule #12: 50S ribosomal protein L16
+Macromolecule #13: 50S ribosomal protein L17
+Macromolecule #14: 50S ribosomal protein L18
+Macromolecule #15: 50S ribosomal protein L19
+Macromolecule #16: 50S ribosomal protein L20
+Macromolecule #17: 50S ribosomal protein L21
+Macromolecule #18: 50S ribosomal protein L22
+Macromolecule #19: 50S ribosomal protein L23
+Macromolecule #20: 50S ribosomal protein L24
+Macromolecule #21: 50S ribosomal protein L25
+Macromolecule #22: 50S ribosomal protein L27
+Macromolecule #23: 50S ribosomal protein L28
+Macromolecule #24: 50S ribosomal protein L29
+Macromolecule #25: 50S ribosomal protein L30
+Macromolecule #26: 50S ribosomal protein L32
+Macromolecule #27: 50S ribosomal protein L33
+Macromolecule #28: 50S ribosomal protein L34
+Macromolecule #29: 50S ribosomal protein L35
+Macromolecule #30: 50S ribosomal protein L36
+Macromolecule #31: 50S ribosomal protein L31
+Macromolecule #33: 30S ribosomal protein S2
+Macromolecule #34: 30S ribosomal protein S3
+Macromolecule #35: 30S ribosomal protein S4
+Macromolecule #36: 30S ribosomal protein S5
+Macromolecule #37: 30S ribosomal protein S6
+Macromolecule #38: 30S ribosomal protein S7
+Macromolecule #39: 30S ribosomal protein S8
+Macromolecule #40: 30S ribosomal protein S9
+Macromolecule #41: 30S ribosomal protein S10
+Macromolecule #42: 30S ribosomal protein S11
+Macromolecule #43: 30S ribosomal protein S12
+Macromolecule #44: 30S ribosomal protein S13
+Macromolecule #45: 30S ribosomal protein S14
+Macromolecule #46: 30S ribosomal protein S15
+Macromolecule #47: 30S ribosomal protein S16
+Macromolecule #48: 30S ribosomal protein S17
+Macromolecule #49: 30S ribosomal protein S18
+Macromolecule #50: 30S ribosomal protein S19
+Macromolecule #51: 30S ribosomal protein S20
+Macromolecule #52: 30S ribosomal protein S21
+Macromolecule #53: ermC Nacent chain
+Macromolecule #58: MAGNESIUM ION
+Macromolecule #59: ERYTHROMYCIN A
+Macromolecule #60: 2-[[[(3~{R},5~{R})-3-azanyl-6-(3-azanylpropylamino)-5-oxidanyl-he...
+Macromolecule #61: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 600 / Average exposure time: 40.0 sec. / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7b5k: |