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- EMDB-17348: E167K RF2 on E. coli 70S release complex with UGG (Structure III) -
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Open data
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Basic information
Entry | ![]() | ||||||||||||||||||||||||||||||
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Title | E167K RF2 on E. coli 70S release complex with UGG (Structure III) | ||||||||||||||||||||||||||||||
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![]() | release factor / translation termination / charge-flip mutation / near-cognate codon recognition / RIBOSOME | ||||||||||||||||||||||||||||||
Function / homology | ![]() translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / stringent response / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / transcriptional attenuation / endoribonuclease inhibitor activity ...translation release factor activity, codon specific / negative regulation of cytoplasmic translational initiation / stringent response / 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 / translational termination / DnaA-L2 complex / 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 / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / DNA endonuclease activity / ribosomal large subunit assembly / transcription antitermination / response to reactive oxygen species / translational initiation / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / 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 / molecular adaptor activity / rRNA binding / negative regulation of translation / 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 | ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.77 Å | ||||||||||||||||||||||||||||||
![]() | Pundir S / Larsson DSD / Selmer M / Sanyal S | ||||||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The compensatory mechanism of a naturally evolved E167K RF2 counteracting the loss of RF1 in bacteria Authors: Pundir S / Larsson DSD / Selmer M / Sanyal S | ||||||||||||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 269.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 82.3 KB 82.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.1 KB | Display | ![]() |
Images | ![]() | 190.3 KB | ||
Filedesc metadata | ![]() | 16.4 KB | ||
Others | ![]() ![]() | 498.3 MB 498.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8p18MC ![]() 8p16C ![]() 8p17C C: citing same article ( M: atomic model generated by this map |
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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
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.83355 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17348_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17348_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Ribosome Release Complex
+Supramolecule #1: Ribosome Release Complex
+Macromolecule #1: 16S rRNA
+Macromolecule #22: mRNA
+Macromolecule #23: tRNA(fMet)
+Macromolecule #24: 23S rRNA
+Macromolecule #25: 5S rRNA
+Macromolecule #2: Small ribosomal subunit protein uS2
+Macromolecule #3: Small ribosomal subunit protein uS3
+Macromolecule #4: Small ribosomal subunit protein uS4
+Macromolecule #5: Small ribosomal subunit protein uS5
+Macromolecule #6: 30S ribosomal protein S6
+Macromolecule #7: 30S ribosomal protein S7
+Macromolecule #8: Small ribosomal subunit protein uS8
+Macromolecule #9: Small ribosomal subunit protein uS9
+Macromolecule #10: Small ribosomal subunit protein uS10
+Macromolecule #11: Small ribosomal subunit protein uS11
+Macromolecule #12: Small ribosomal subunit protein uS12
+Macromolecule #13: Small ribosomal subunit protein uS13
+Macromolecule #14: Small ribosomal subunit protein uS14
+Macromolecule #15: Small ribosomal subunit protein uS15
+Macromolecule #16: Small ribosomal subunit protein bS16
+Macromolecule #17: Small ribosomal subunit protein uS17
+Macromolecule #18: Small ribosomal subunit protein bS18
+Macromolecule #19: Small ribosomal subunit protein uS19
+Macromolecule #20: Small ribosomal subunit protein bS20
+Macromolecule #21: Small ribosomal subunit protein bS21
+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 L13
+Macromolecule #32: 50S ribosomal protein L14
+Macromolecule #33: 50S ribosomal protein L15
+Macromolecule #34: Large ribosomal subunit protein uL16
+Macromolecule #35: 50S ribosomal protein L17
+Macromolecule #36: 50S ribosomal protein L18
+Macromolecule #37: 50S ribosomal protein L19
+Macromolecule #38: 50S ribosomal protein L20
+Macromolecule #39: 50S ribosomal protein L21
+Macromolecule #40: 50S ribosomal protein L22
+Macromolecule #41: 50S ribosomal protein L23
+Macromolecule #42: 50S ribosomal protein L24
+Macromolecule #43: 50S ribosomal protein L25
+Macromolecule #44: 50S ribosomal protein L27
+Macromolecule #45: 50S ribosomal protein L28
+Macromolecule #46: 50S ribosomal protein L29
+Macromolecule #47: 50S ribosomal protein L30
+Macromolecule #48: 50S ribosomal protein L32
+Macromolecule #49: 50S ribosomal protein L33
+Macromolecule #50: 50S ribosomal protein L34
+Macromolecule #51: 50S ribosomal protein L35
+Macromolecule #52: 50S ribosomal protein L36
+Macromolecule #53: Large ribosomal subunit protein bL31
+Macromolecule #54: 50S ribosomal protein L11
+Macromolecule #55: Peptide chain release factor RF2
+Macromolecule #56: 50S ribosomal protein L9
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: SPERMIDINE
+Macromolecule #59: POTASSIUM ION
+Macromolecule #60: 1,4-DIAMINOBUTANE
+Macromolecule #61: SPERMINE
+Macromolecule #62: ZINC ION
+Macromolecule #63: water
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.1 mg/mL | |||||||||||||||||||||||||||
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Buffer | pH: 7.5 Component:
Details: HEPES-polymix buffer (pH-7.5) | |||||||||||||||||||||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY ARRAY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa | |||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||||||||||||||
Details | E167K mutant RF2 bound to the ribosome release complex containing Trp UGG codon in the A-site |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3840 pixel / Digitization - Dimensions - Height: 3712 pixel / Number grids imaged: 1 / Number real images: 8135 / Average electron dose: 38.14 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
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 |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 78.7 | ||||||||||||||||||
Output model | ![]() PDB-8p18: |