+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18320 | |||||||||
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Title | E. coli ApdP-stalled ribosomal complex | |||||||||
Map data | Postprocessed final map | |||||||||
Sample |
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Keywords | Stalling / nascent chain / translation arrest / regulation / RIBOSOME | |||||||||
Function / homology | Function and homology information mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation ...mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / response to reactive oxygen species / cytosolic ribosome assembly / regulation of cell growth / maintenance of translational fidelity / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / regulation of translation / small ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Sinorhizobium medicae (bacteria) / Escherichia coli BW25113 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.2 Å | |||||||||
Authors | Morici M / Wilson DN | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. Authors: Martino Morici / Sara Gabrielli / Keigo Fujiwara / Helge Paternoga / Bertrand Beckert / Lars V Bock / Shinobu Chiba / Daniel N Wilson / Abstract: Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein ...Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein localization machinery components. Here we determine cryo-EM structures of ribosomes stalled on RAPP arrest motifs in both Bacillus subtilis and Escherichia coli. Together with molecular dynamics simulations, our structures reveal that the RAPP motifs allow full accommodation of the A-site tRNA, but prevent the subsequent peptide bond from forming. Our data support a model where the RAP in the P-site interacts and stabilizes a single hydrogen atom on the Pro-tRNA in the A-site, thereby preventing an optimal geometry for the nucleophilic attack required for peptide bond formation to occur. This mechanism to short circuit the ribosomal peptidyltransferase activity is likely to operate for the majority of other RAPP-like arrest peptides found across diverse bacterial phylogenies. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18320.map.gz | 49.8 MB | EMDB map data format | |
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Header (meta data) | emd-18320-v30.xml emd-18320.xml | 71.1 KB 71.1 KB | Display Display | EMDB header |
Images | emd_18320.png | 61.1 KB | ||
Filedesc metadata | emd-18320.cif.gz | 13.4 KB | ||
Others | emd_18320_additional_1.map.gz emd_18320_additional_2.map.gz emd_18320_half_map_1.map.gz emd_18320_half_map_2.map.gz | 140 MB 95.3 MB 140.4 MB 140.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18320 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18320 | HTTPS FTP |
-Related structure data
Related structure data | 8qbtMC 8qcqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_18320.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed final map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Preprocessed map
File | emd_18320_additional_1.map | ||||||||||||
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Annotation | Preprocessed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Filtered 3D map on the base of local...
File | emd_18320_additional_2.map | ||||||||||||
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Annotation | Filtered 3D map on the base of local resolution as calculated by Bsoft | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 1
File | emd_18320_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_18320_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : E. coli ApdP-stalled ribosomal complex
+Supramolecule #1: E. coli ApdP-stalled ribosomal complex
+Macromolecule #1: 23S rRNA
+Macromolecule #2: 5S rRNA
+Macromolecule #30: 16S rRNA
+Macromolecule #47: mRNA
+Macromolecule #48: Pro-tRNA
+Macromolecule #49: Ala-tRNA
+Macromolecule #3: Large ribosomal subunit protein uL2
+Macromolecule #4: 50S ribosomal protein L3
+Macromolecule #5: Large ribosomal subunit protein uL4
+Macromolecule #6: Large ribosomal subunit protein uL5
+Macromolecule #7: Large ribosomal subunit protein uL6
+Macromolecule #8: Large ribosomal subunit protein bL9
+Macromolecule #9: Large ribosomal subunit protein uL13
+Macromolecule #10: Large ribosomal subunit protein uL14
+Macromolecule #11: 50S ribosomal protein L15
+Macromolecule #12: 50S ribosomal protein L16
+Macromolecule #13: Large ribosomal subunit protein bL17
+Macromolecule #14: Large ribosomal subunit protein uL18
+Macromolecule #15: Large ribosomal subunit protein bL19
+Macromolecule #16: Large ribosomal subunit protein bL20
+Macromolecule #17: Large ribosomal subunit protein bL21
+Macromolecule #18: Large ribosomal subunit protein uL22
+Macromolecule #19: Large ribosomal subunit protein uL23
+Macromolecule #20: Large ribosomal subunit protein uL24
+Macromolecule #21: 50S ribosomal protein L25
+Macromolecule #22: Large ribosomal subunit protein bL27
+Macromolecule #23: Large ribosomal subunit protein bL28
+Macromolecule #24: Large ribosomal subunit protein uL29
+Macromolecule #25: Large ribosomal subunit protein uL30
+Macromolecule #26: Large ribosomal subunit protein bL32
+Macromolecule #27: Large ribosomal subunit protein bL33
+Macromolecule #28: Large ribosomal subunit protein bL34
+Macromolecule #29: Large ribosomal subunit protein bL35
+Macromolecule #31: 30S ribosomal protein S2
+Macromolecule #32: Small ribosomal subunit protein uS5
+Macromolecule #33: 30S ribosomal protein S6, fully modified isoform
+Macromolecule #34: 30S ribosomal protein S7
+Macromolecule #35: Small ribosomal subunit protein uS8
+Macromolecule #36: Small ribosomal subunit protein uS9
+Macromolecule #37: 30S ribosomal protein S11
+Macromolecule #38: 30S ribosomal protein S12
+Macromolecule #39: Small ribosomal subunit protein uS13
+Macromolecule #40: Small ribosomal subunit protein uS14
+Macromolecule #41: Small ribosomal subunit protein uS15
+Macromolecule #42: Small ribosomal subunit protein uS17
+Macromolecule #43: Small ribosomal subunit protein bS18
+Macromolecule #44: Small ribosomal subunit protein uS19
+Macromolecule #45: 30S ribosomal protein S20
+Macromolecule #46: Small ribosomal subunit protein bS21
+Macromolecule #50: Large ribosomal subunit protein bL36A
+Macromolecule #51: ApdP nascent chain
+Macromolecule #52: MAGNESIUM ION
+Macromolecule #53: POTASSIUM ION
+Macromolecule #54: PROLINE
+Macromolecule #55: ZINC ION
+Macromolecule #56: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 75.6 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER Details: Exprimental unpublished map from our lab from an analogous ample, previously low-pass filtered |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 205838 |