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Yorodumi- EMDB-10908: Structure of the P+0 ArfB-ribosome complex in the post-hydrolysis... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10908 | |||||||||
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Title | Structure of the P+0 ArfB-ribosome complex in the post-hydrolysis state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | translation / ribosome / rescue / release | |||||||||
Function / homology | Function and homology information translation release factor activity / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination ...translation release factor activity / peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / ribosome biogenesis / cytoplasmic translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Apis mellifera (honey bee) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Chan K-H / Petrychenko V | |||||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Mechanism of ribosome rescue by alternative ribosome-rescue factor B. Authors: Kai-Hsin Chan / Valentyn Petrychenko / Claudia Mueller / Cristina Maracci / Wolf Holtkamp / Daniel N Wilson / Niels Fischer / Marina V Rodnina / Abstract: Alternative ribosome-rescue factor B (ArfB) rescues ribosomes stalled on non-stop mRNAs by releasing the nascent polypeptide from the peptidyl-tRNA. By rapid kinetics we show that ArfB selects ...Alternative ribosome-rescue factor B (ArfB) rescues ribosomes stalled on non-stop mRNAs by releasing the nascent polypeptide from the peptidyl-tRNA. By rapid kinetics we show that ArfB selects ribosomes stalled on short truncated mRNAs, rather than on longer mRNAs mimicking pausing on rare codon clusters. In combination with cryo-electron microscopy we dissect the multistep rescue pathway of ArfB, which first binds to ribosomes very rapidly regardless of the mRNA length. The selectivity for shorter mRNAs arises from the subsequent slow engagement step, as it requires longer mRNA to shift to enable ArfB binding. Engagement results in specific interactions of the ArfB C-terminal domain with the mRNA entry channel, which activates peptidyl-tRNA hydrolysis by the N-terminal domain. These data reveal how protein dynamics translate into specificity of substrate recognition and provide insights into the action of a putative rescue factor in mitochondria. | |||||||||
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_10908.map.gz | 116.9 MB | EMDB map data format | |
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Header (meta data) | emd-10908-v30.xml emd-10908.xml | 82.9 KB 82.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10908_fsc.xml | 11.5 KB | Display | FSC data file |
Images | emd_10908.png | 167.2 KB | ||
Masks | emd_10908_msk_1.map | 129.7 MB | Mask map | |
Filedesc metadata | emd-10908.cif.gz | 14.6 KB | ||
Others | emd_10908_half_map_1.map.gz emd_10908_half_map_2.map.gz | 102.2 MB 102.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10908 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10908 | HTTPS FTP |
-Related structure data
Related structure data | 6ysuMC 6ysrC 6yssC 6ystC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10443 (Title: Mechanism of Ribosome Rescue by Alternative Release Factor B Data size: 788.2 Data #1: Motion-corrected, dose-weighted micrographs & polished particles of P+9 E. coli ribosome-ArfB complex [micrographs - single frame] Data #2: Motion-corrected, dose-weighted micrographs & extracted particles of P+0 E. coli ribosome-ArfB complex [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10908.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.072 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10908_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10908_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10908_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Post-hydrolysis state of E. coli ribosome P+0 70S-ArfB-Api137-tRN...
+Supramolecule #1: Post-hydrolysis state of E. coli ribosome P+0 70S-ArfB-Api137-tRN...
+Supramolecule #2: Post-hydrolysis state of E. coli ribosome P+0 70S-ArfB-Api137-tRN...
+Supramolecule #3: Post-hydrolysis state of E. coli ribosome P+0 70S-ArfB-Api137-tRN...
+Macromolecule #1: 50S ribosomal protein L32
+Macromolecule #2: 50S ribosomal protein L33
+Macromolecule #3: 50S ribosomal protein L34
+Macromolecule #4: 50S ribosomal protein L35
+Macromolecule #5: 50S ribosomal protein L36
+Macromolecule #6: 50S ribosomal protein L10
+Macromolecule #9: 50S ribosomal protein L2
+Macromolecule #10: 50S ribosomal protein L3
+Macromolecule #11: 50S ribosomal protein L4
+Macromolecule #12: 50S ribosomal protein L5
+Macromolecule #13: 50S ribosomal protein L6
+Macromolecule #14: 50S ribosomal protein L9
+Macromolecule #15: 50S ribosomal protein L11
+Macromolecule #16: 50S ribosomal protein L13
+Macromolecule #17: 50S ribosomal protein L14
+Macromolecule #18: 50S ribosomal protein L15
+Macromolecule #19: 50S ribosomal protein L16
+Macromolecule #20: 50S ribosomal protein L17
+Macromolecule #21: 50S ribosomal protein L18
+Macromolecule #22: 50S ribosomal protein L19
+Macromolecule #23: 50S ribosomal protein L20
+Macromolecule #24: 50S ribosomal protein L21
+Macromolecule #25: 50S ribosomal protein L22
+Macromolecule #26: 50S ribosomal protein L23
+Macromolecule #27: 50S ribosomal protein L24
+Macromolecule #28: 50S ribosomal protein L25
+Macromolecule #29: 50S ribosomal protein L27
+Macromolecule #30: 50S ribosomal protein L28
+Macromolecule #31: 50S ribosomal protein L29
+Macromolecule #32: 50S ribosomal protein L30
+Macromolecule #34: 30S ribosomal protein S2
+Macromolecule #35: 30S ribosomal protein S3
+Macromolecule #36: 30S ribosomal protein S4
+Macromolecule #37: 30S ribosomal protein S5
+Macromolecule #38: 30S ribosomal protein S6
+Macromolecule #39: 30S ribosomal protein S7
+Macromolecule #40: 30S ribosomal protein S8
+Macromolecule #41: 30S ribosomal protein S9
+Macromolecule #42: 30S ribosomal protein S10
+Macromolecule #43: 30S ribosomal protein S11
+Macromolecule #44: 30S ribosomal protein S12
+Macromolecule #45: 30S ribosomal protein S13
+Macromolecule #46: 30S ribosomal protein S14
+Macromolecule #47: 30S ribosomal protein S15
+Macromolecule #48: 30S ribosomal protein S16
+Macromolecule #49: 30S ribosomal protein S17
+Macromolecule #50: 30S ribosomal protein S18
+Macromolecule #51: 30S ribosomal protein S19
+Macromolecule #52: 30S ribosomal protein S20
+Macromolecule #53: 30S ribosomal protein S21
+Macromolecule #54: Api137
+Macromolecule #57: Alternative stalled-ribosome rescue factor B
+Macromolecule #7: 23S ribosomal RNA
+Macromolecule #8: 5S ribosomal RNA
+Macromolecule #33: 16S ribosomal RNA
+Macromolecule #55: P-site tRNAPhe
+Macromolecule #56: RNA (5'-R(P*AP*UP*GP*UP*UP*C)-3')
+Macromolecule #58: MAGNESIUM ION
+Macromolecule #59: ZINC ION
+Macromolecule #60: SODIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: 50 mM HEPES, 30 mM KCl, 7 mM MgCl2, 0.1 % w/v DDM |
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Grid | Model: Quantifoil R3/3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 2.3000000000000003 µm / Calibrated defocus min: 1.1 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 59000 |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 25.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL | ||||||||||
Output model | PDB-6ysu: |