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Yorodumi- EMDB-8505: Structural Basis of Co-translational Quality Control by ArfA and ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8505 | |||||||||
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Title | Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome | |||||||||
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Sample |
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Function / homology | Function and homology information translation release factor activity, codon specific / stringent response / ribosomal large subunit binding / 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 / stringent response / ribosomal large subunit binding / 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 / rescue of stalled ribosome / 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 / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Zeng F / Chen Y / Remis J / Shekhar M / Phillips JC / Tajkhorshid E / Jin H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2017 Title: Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome. Authors: Fuxing Zeng / Yanbo Chen / Jonathan Remis / Mrinal Shekhar / James C Phillips / Emad Tajkhorshid / Hong Jin / Abstract: Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs ...Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown. Here we report an electron cryo-microscopy structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop mRNA. The structure, which is consistent with our kinetic and biochemical data, reveals the molecular interactions that enable ArfA to specifically recruit RF2, not RF1, into the ribosome and to enable RF2 to release the truncated protein product in this co-translational quality control pathway. The positively charged C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome. Furthermore, binding of ArfA and RF2 induces conformational changes in the ribosomal decoding centre that are similar to those seen in other protein-involved decoding processes. Specific interactions between residues in the N-terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent conformation for peptide release. Our findings provide a framework for understanding recognition of the translational state of the ribosome by new proteins, and expand our knowledge of the decoding potential of the ribosome. | |||||||||
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_8505.map.gz | 202.4 MB | EMDB map data format | |
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Header (meta data) | emd-8505-v30.xml emd-8505.xml | 116.6 KB 116.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8505_fsc.xml | 13.4 KB | Display | FSC data file |
Images | emd_8505.png | 99.8 KB | ||
Others | emd_8505_half_map_1.map.gz emd_8505_half_map_2.map.gz | 171.5 MB 171.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8505 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8505 | HTTPS FTP |
-Validation report
Summary document | emd_8505_validation.pdf.gz | 930.9 KB | Display | EMDB validaton report |
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Full document | emd_8505_full_validation.pdf.gz | 930.5 KB | Display | |
Data in XML | emd_8505_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | emd_8505_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8505 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8505 | HTTPS FTP |
-Related structure data
Related structure data | 5u4iMC 8506C 5u4jC C: citing same article (ref.) M: atomic model generated by this map |
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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_8505.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.193 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_8505_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_8505_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Non-stop ribosomal complex with ArfA and RF2
+Supramolecule #1: Non-stop ribosomal complex with ArfA and RF2
+Supramolecule #2: 30S subunit
+Supramolecule #3: 50S subunit
+Supramolecule #11: 30S ribosomal protein S2
+Supramolecule #49: 50S ribosomal protein L25
+Supramolecule #4: Alternative ribosome-rescue factor A
+Supramolecule #5: Peptide chain release factor 2
+Supramolecule #6: P-site or E-site fMet-tRNA(fMet)
+Supramolecule #7: mRNA
+Supramolecule #8: 23S rRNA
+Supramolecule #9: 50S ribosomal protein L2
+Supramolecule #10: 16S rRNA
+Supramolecule #12: 30S ribosomal protein S3
+Supramolecule #13: 30S ribosomal protein S4
+Supramolecule #14: 30S ribosomal protein S5
+Supramolecule #15: 30S ribosomal protein S6
+Supramolecule #16: 30S ribosomal protein S7
+Supramolecule #17: 30S ribosomal protein S8
+Supramolecule #18: 30S ribosomal protein S9
+Supramolecule #19: 30S ribosomal protein S10
+Supramolecule #20: 30S ribosomal protein S11
+Supramolecule #21: 30S ribosomal protein S12
+Supramolecule #22: 30S ribosomal protein S13
+Supramolecule #23: 30S ribosomal protein S14
+Supramolecule #24: 30S ribosomal protein S15
+Supramolecule #25: 30S ribosomal protein S16
+Supramolecule #26: 30S ribosomal protein S17
+Supramolecule #27: 30S ribosomal protein S18
+Supramolecule #28: 30S ribosomal protein S19
+Supramolecule #29: 30S ribosomal protein S20
+Supramolecule #30: 30S ribosomal protein S21
+Supramolecule #31: 50S ribosomal protein L3
+Supramolecule #32: 50S ribosomal protein L4
+Supramolecule #33: 50S ribosomal protein L5
+Supramolecule #34: 50S ribosomal protein L6
+Supramolecule #35: 50S ribosomal protein L9
+Supramolecule #36: 50S ribosomal protein L11
+Supramolecule #37: 50S ribosomal protein L13
+Supramolecule #38: 50S ribosomal protein L14
+Supramolecule #39: 50S ribosomal protein L15
+Supramolecule #40: 50S ribosomal protein L16
+Supramolecule #41: 50S ribosomal protein L17
+Supramolecule #42: 50S ribosomal protein L18
+Supramolecule #43: 50S ribosomal protein L19
+Supramolecule #44: 50S ribosomal protein L20
+Supramolecule #45: 50S ribosomal protein L21
+Supramolecule #46: 50S ribosomal protein L22
+Supramolecule #47: 50S ribosomal protein L23
+Supramolecule #48: 50S ribosomal protein L24
+Supramolecule #50: 50S ribosomal protein L27
+Supramolecule #51: 50S ribosomal protein L28
+Supramolecule #52: 50S ribosomal protein L29
+Supramolecule #53: 50S ribosomal protein L30
+Supramolecule #54: 50S ribosomal protein L32
+Supramolecule #55: 50S ribosomal protein L33
+Supramolecule #56: 50S ribosomal protein L34
+Supramolecule #57: 50S ribosomal protein L35
+Supramolecule #58: 50S ribosomal protein L36
+Supramolecule #59: 5S rRNA
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #32: 16S rRNA
+Macromolecule #55: P-site or E-site fMet-tRNA(fMet)
+Macromolecule #56: 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 L11
+Macromolecule #10: 50S ribosomal protein L13
+Macromolecule #11: 50S ribosomal protein L14
+Macromolecule #12: 50S ribosomal protein L15
+Macromolecule #13: 50S ribosomal protein L16
+Macromolecule #14: 50S ribosomal protein L17
+Macromolecule #15: 50S ribosomal protein L18
+Macromolecule #16: 50S ribosomal protein L19
+Macromolecule #17: 50S ribosomal protein L20
+Macromolecule #18: 50S ribosomal protein L21
+Macromolecule #19: 50S ribosomal protein L22
+Macromolecule #20: 50S ribosomal protein L23
+Macromolecule #21: 50S ribosomal protein L24
+Macromolecule #22: 50S ribosomal protein L25
+Macromolecule #23: 50S ribosomal protein L27
+Macromolecule #24: 50S ribosomal protein L28
+Macromolecule #25: 50S ribosomal protein L29
+Macromolecule #26: 50S ribosomal protein L30
+Macromolecule #27: 50S ribosomal protein L32
+Macromolecule #28: 50S ribosomal protein L33
+Macromolecule #29: 50S ribosomal protein L34
+Macromolecule #30: 50S ribosomal protein L35
+Macromolecule #31: 50S ribosomal protein L36
+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: Peptide chain release factor 2
+Macromolecule #54: Alternative ribosome-rescue factor A
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-2/0.5 4C / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 4-25 / Average exposure time: 6.0 sec. / Average electron dose: 20.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 83822 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Target criteria: Average FSC |
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Output model | PDB-5u4i: |