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Yorodumi- EMDB-7970: E.coli RF1 bound to E.coli 70S ribosome in response to UAU sense ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7970 | |||||||||
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Title | E.coli RF1 bound to E.coli 70S ribosome in response to UAU sense A-site codon | |||||||||
Map data | E.coli RF1 bound to E.coli 70S ribosome in response to UAU sense A-site codon | |||||||||
Sample |
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Keywords | RF1 / ribosome / sense codon / cryo-EM | |||||||||
Function / homology | Function and homology information translation release factor activity, codon specific / ribosomal large subunit assembly / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit ...translation release factor activity, codon specific / ribosomal large subunit assembly / maintenance of translational fidelity / response to radiation / mRNA 5'-UTR binding / large ribosomal subunit / 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 / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / RNA binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Svidritskiy E / Demo G | |||||||||
Funding support | United States, 1 items
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Citation | Journal: J Biol Chem / Year: 2018 Title: Mechanism of premature translation termination on a sense codon. Authors: Egor Svidritskiy / Gabriel Demo / Andrei A Korostelev / Abstract: Accurate translation termination by release factors (RFs) is critical for the integrity of cellular proteomes. Premature termination on sense codons, for example, results in truncated proteins, whose ...Accurate translation termination by release factors (RFs) is critical for the integrity of cellular proteomes. Premature termination on sense codons, for example, results in truncated proteins, whose accumulation could be detrimental to the cell. Nevertheless, some sense codons are prone to triggering premature termination, but the structural basis for this is unclear. To investigate premature termination, we determined a cryo-EM structure of the 70S ribosome bound with RF1 in response to a UAU (Tyr) sense codon. The structure reveals that RF1 recognizes a UAU codon similarly to a UAG stop codon, suggesting that sense codons induce premature termination because they structurally mimic a stop codon. Hydrophobic interaction between the nucleobase of U3 (the third position of the UAU codon) and conserved Ile-196 in RF1 is important for misreading the UAU codon. Analyses of RNA binding in ribonucleoprotein complexes or by amino acids reveal that Ile-U packing is a frequent protein-RNA-binding motif with key functional implications. We discuss parallels with eukaryotic translation termination by the release factor eRF1. | |||||||||
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_7970.map.gz | 117.8 MB | EMDB map data format | |
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Header (meta data) | emd-7970-v30.xml emd-7970.xml | 75 KB 75 KB | Display Display | EMDB header |
Images | emd_7970.png | 85.8 KB | ||
Filedesc metadata | emd-7970.cif.gz | 14.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7970 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7970 | HTTPS FTP |
-Validation report
Summary document | emd_7970_validation.pdf.gz | 467.3 KB | Display | EMDB validaton report |
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Full document | emd_7970_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | emd_7970_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | emd_7970_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7970 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7970 | HTTPS FTP |
-Related structure data
Related structure data | 6dncMC 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_7970.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E.coli RF1 bound to E.coli 70S ribosome in response to UAU sense A-site codon | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.927 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : RF1 bound to the 70S ribosome in response to sense UAU A-site codon
+Supramolecule #1: RF1 bound to the 70S ribosome in response to sense UAU A-site codon
+Supramolecule #2: Peptide chain release factor 1
+Macromolecule #1: 16S ribosomal RNA
+Macromolecule #2: 23S ribosomal RNA
+Macromolecule #3: 5S ribosomal RNA
+Macromolecule #4: tRNA(fMet)
+Macromolecule #37: mRNA
+Macromolecule #5: 50S ribosomal protein L1
+Macromolecule #6: 50S ribosomal protein L2
+Macromolecule #7: 50S ribosomal protein L3
+Macromolecule #8: 50S ribosomal protein L4
+Macromolecule #9: 50S ribosomal protein L5
+Macromolecule #10: 50S ribosomal protein L6
+Macromolecule #11: 50S ribosomal protein L9
+Macromolecule #12: 50S ribosomal protein L10
+Macromolecule #13: 50S ribosomal protein L11
+Macromolecule #14: 50S ribosomal protein L13
+Macromolecule #15: 50S ribosomal protein L14
+Macromolecule #16: 50S ribosomal protein L15
+Macromolecule #17: 50S ribosomal protein L16
+Macromolecule #18: 50S ribosomal protein L17
+Macromolecule #19: 50S ribosomal protein L18
+Macromolecule #20: 50S ribosomal protein L19
+Macromolecule #21: 50S ribosomal protein L20
+Macromolecule #22: 50S ribosomal protein L21
+Macromolecule #23: 50S ribosomal protein L22
+Macromolecule #24: 50S ribosomal protein L23
+Macromolecule #25: 50S ribosomal protein L24
+Macromolecule #26: 50S ribosomal protein L25
+Macromolecule #27: 50S ribosomal protein L27
+Macromolecule #28: 50S ribosomal protein L28
+Macromolecule #29: 50S ribosomal protein L29
+Macromolecule #30: 50S ribosomal protein L30
+Macromolecule #31: 50S ribosomal protein L31
+Macromolecule #32: 50S ribosomal protein L32
+Macromolecule #33: 50S ribosomal protein L33
+Macromolecule #34: 50S ribosomal protein L34
+Macromolecule #35: 50S ribosomal protein L35
+Macromolecule #36: 50S ribosomal protein L36
+Macromolecule #38: Peptide chain release factor 1
+Macromolecule #39: 30S ribosomal protein S2
+Macromolecule #40: 30S ribosomal protein S3
+Macromolecule #41: 30S ribosomal protein S4
+Macromolecule #42: 30S ribosomal protein S5
+Macromolecule #43: 30S ribosomal protein S6
+Macromolecule #44: 30S ribosomal protein S7
+Macromolecule #45: 30S ribosomal protein S8
+Macromolecule #46: 30S ribosomal protein S9
+Macromolecule #47: 30S ribosomal protein S10
+Macromolecule #48: 30S ribosomal protein S11
+Macromolecule #49: 30S ribosomal protein S12
+Macromolecule #50: 30S ribosomal protein S13
+Macromolecule #51: 30S ribosomal protein S14
+Macromolecule #52: 30S ribosomal protein S15
+Macromolecule #53: 30S ribosomal protein S16
+Macromolecule #54: 30S ribosomal protein S17
+Macromolecule #55: 30S ribosomal protein S18
+Macromolecule #56: 30S ribosomal protein S19
+Macromolecule #57: 30S ribosomal protein S20
+Macromolecule #58: 30S ribosomal protein S21
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 Component:
Details: 20 mM Tris-HCl, 100 mM NH4Cl, 20.5 mM MgCl2, 0.5 mM EDTA, 6 mM beta-mercaptoethanol | ||||||||||||
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Grid | Model: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR Details: PELCO easiGlow glow discharge unit, negative 20 mA. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 3-42 / Number grids imaged: 1 / Number real images: 3963 / Average electron dose: 0.5 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 22000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 200 / Target criteria: Correlation coefficient |
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Output model | PDB-6dnc: |