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Yorodumi- EMDB-8506: Structural Basis of Co-translational Quality Control by ArfA and ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8506 | |||||||||
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Title | Structural Basis of Co-translational Quality Control by ArfA and RF2 Binding to Ribosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ribosome / ArfA / RF2 / nonstop translation | |||||||||
Function / homology | Function and homology information translation release factor activity, codon specific / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / translational termination / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / rescue of stalled ribosome / positive regulation of RNA splicing ...translation release factor activity, codon specific / ribosomal large subunit binding / misfolded RNA binding / Group I intron splicing / RNA folding / translational termination / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / rescue of stalled ribosome / positive regulation of RNA splicing / transcription antitermination / DNA-templated transcription termination / maintenance of translational fidelity / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / viral translational frameshifting / translation / response to antibiotic / mRNA binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Zeng F / Chen Y | |||||||||
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_8506.map.gz | 202.2 MB | EMDB map data format | |
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Header (meta data) | emd-8506-v30.xml emd-8506.xml | 38 KB 38 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8506_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_8506.png | 97.3 KB | ||
Filedesc metadata | emd-8506.cif.gz | 9.9 KB | ||
Others | emd_8506_half_map_1.map.gz emd_8506_half_map_2.map.gz | 171.4 MB 171.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8506 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8506 | HTTPS FTP |
-Validation report
Summary document | emd_8506_validation.pdf.gz | 968.9 KB | Display | EMDB validaton report |
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Full document | emd_8506_full_validation.pdf.gz | 968.4 KB | Display | |
Data in XML | emd_8506_validation.xml.gz | 21 KB | Display | |
Data in CIF | emd_8506_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8506 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8506 | HTTPS FTP |
-Related structure data
Related structure data | 5u4jMC 8505C 5u4iC 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_8506.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: half map 1
File | emd_8506_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_8506_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
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 #4: Alternative ribosome-rescue factor A
+Supramolecule #5: Peptide chain release factor 2
+Supramolecule #6: P-site tRNA fMet
+Supramolecule #7: mRNA
+Supramolecule #8: 23S rRNA
+Supramolecule #9: 16S rRNA
+Supramolecule #10: 30S ribosomal protein S3
+Supramolecule #11: 30S ribosomal protein S4
+Supramolecule #12: 30S ribosomal protein S5
+Supramolecule #13: 30S ribosomal protein S12
+Macromolecule #1: 16S rRNA
+Macromolecule #2: 23S rRNA
+Macromolecule #6: mRNA
+Macromolecule #7: P-site tRNA fMet
+Macromolecule #3: 30S ribosomal protein S3
+Macromolecule #4: 30S ribosomal protein S4
+Macromolecule #5: 30S ribosomal protein S5
+Macromolecule #8: 30S ribosomal protein S12
+Macromolecule #9: Peptide chain release factor 2
+Macromolecule #10: Alternative ribosome-rescue factor A
-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 / Details: Grids were blotted for 3.5 s. |
-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: 0.7000000000000001 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 108.501 / Target criteria: Average FSC |
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Output model | PDB-5u4j: |