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Yorodumi- EMDB-14454: 70S E. coli ribosome with an extended uL23 loop from Candidatus m... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14454 | |||||||||
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Title | 70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia and a stalled filamin domain 5 nascent chain | |||||||||
Map data | Sharpened map | |||||||||
Sample |
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Function / homology | Function and homology information regulation of pseudopodium assembly / anterior cell cortex / pseudopodium assembly / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex / phototaxis / macropinocytic cup / protein kinase B binding ...regulation of pseudopodium assembly / anterior cell cortex / pseudopodium assembly / sorocarp development / posterior cell cortex / chemotaxis to cAMP / lateral cell cortex / phototaxis / macropinocytic cup / protein kinase B binding / actin crosslink formation / thermotaxis / hyperosmotic response / mitogen-activated protein kinase binding / lamellipodium assembly / phagocytic cup / cortical actin cytoskeleton / cell leading edge / pseudopodium / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / negative regulation of cytoplasmic translation / phagocytosis / DnaA-L2 complex / translation repressor activity / response to cAMP / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / extracellular matrix / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / : / cytosolic ribosome assembly / cell motility / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / small GTPase binding / ribosomal large subunit assembly / actin filament binding / cell migration / large ribosomal subunit rRNA binding / large ribosomal subunit / cell cortex / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / actin cytoskeleton organization / negative regulation of translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / negative regulation of DNA-templated transcription / DNA binding / RNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) / Escherichia coli (E. coli) / Dictyostelium discoideum (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.29 Å | |||||||||
Authors | Mitropoulou A / Plessa E / Wlodarski T / Ahn M / Sidhu H / Becker TA / Beckmann R / Cabrita LD / Christodoulou J | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Modulating co-translational protein folding by rational design and ribosome engineering. Authors: Minkoo Ahn / Tomasz Włodarski / Alkistis Mitropoulou / Sammy H S Chan / Haneesh Sidhu / Elena Plessa / Thomas A Becker / Nediljko Budisa / Christopher A Waudby / Roland Beckmann / Anaïs M ...Authors: Minkoo Ahn / Tomasz Włodarski / Alkistis Mitropoulou / Sammy H S Chan / Haneesh Sidhu / Elena Plessa / Thomas A Becker / Nediljko Budisa / Christopher A Waudby / Roland Beckmann / Anaïs M E Cassaignau / Lisa D Cabrita / John Christodoulou / Abstract: Co-translational folding is a fundamental process for the efficient biosynthesis of nascent polypeptides that emerge through the ribosome exit tunnel. To understand how this process is modulated by ...Co-translational folding is a fundamental process for the efficient biosynthesis of nascent polypeptides that emerge through the ribosome exit tunnel. To understand how this process is modulated by the shape and surface of the narrow tunnel, we have rationally engineered three exit tunnel protein loops (uL22, uL23 and uL24) of the 70S ribosome by CRISPR/Cas9 gene editing, and studied the co-translational folding of an immunoglobulin-like filamin domain (FLN5). Our thermodynamics measurements employing F/N/methyl-TROSY NMR spectroscopy together with cryo-EM and molecular dynamics simulations reveal how the variations in the lengths of the loops present across species exert their distinct effects on the free energy of FLN5 folding. A concerted interplay of the uL23 and uL24 loops is sufficient to alter co-translational folding energetics, which we highlight by the opposite folding outcomes resulting from their extensions. These subtle modulations occur through a combination of the steric effects relating to the shape of the tunnel, the dynamic interactions between the ribosome surface and the unfolded nascent chain, and its altered exit pathway within the vestibule. These results illustrate the role of the exit tunnel structure in co-translational folding, and provide principles for how to remodel it to elicit a desired folding outcome. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14454.map.gz | 122 MB | EMDB map data format | |
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Header (meta data) | emd-14454-v30.xml emd-14454.xml | 40 KB 40 KB | Display Display | EMDB header |
Images | emd_14454.png | 172.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14454 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14454 | HTTPS FTP |
-Related structure data
Related structure data | 7z20MC 7zodC 7zp8C 7zq5C 7zq6C 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_14454.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : ribosomal nascent chain of FLN5
+Supramolecule #1: ribosomal nascent chain of FLN5
+Macromolecule #1: 50S ribosomal protein L28
+Macromolecule #2: 50S ribosomal protein L29
+Macromolecule #3: 50S ribosomal protein L30
+Macromolecule #4: 50S ribosomal protein L32
+Macromolecule #5: 50S ribosomal protein L33
+Macromolecule #6: 50S ribosomal protein L34
+Macromolecule #7: 50S ribosomal protein L35
+Macromolecule #8: 50S ribosomal protein L36
+Macromolecule #11: 50S ribosomal protein L2
+Macromolecule #12: 50S ribosomal protein L3
+Macromolecule #13: 50S ribosomal protein L4
+Macromolecule #14: 50S ribosomal protein L5
+Macromolecule #15: 50S ribosomal protein L6
+Macromolecule #16: 50S ribosomal protein L9
+Macromolecule #17: 50S ribosomal protein L13
+Macromolecule #18: 50S ribosomal protein L14
+Macromolecule #19: 50S ribosomal protein L15
+Macromolecule #20: 50S ribosomal protein L16
+Macromolecule #21: 50S ribosomal protein L17
+Macromolecule #22: 50S ribosomal protein L18
+Macromolecule #23: 50S ribosomal protein L19
+Macromolecule #24: 50S ribosomal protein L20
+Macromolecule #25: 50S ribosomal protein L21
+Macromolecule #26: 50S ribosomal protein L22
+Macromolecule #27: 50S ribosomal protein L23
+Macromolecule #28: 50S ribosomal protein L24
+Macromolecule #29: 50S ribosomal protein L25
+Macromolecule #30: 50S ribosomal protein L27
+Macromolecule #32: Gelation factor
+Macromolecule #9: 5S rRNA
+Macromolecule #10: 23S rRNA
+Macromolecule #31: Pro-tRNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN 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: 2.5 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.8 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
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Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 547000 |