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Yorodumi- EMDB-29622: Cryo-EM structure of an E. coli rotated ribosome complex bound wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29622 | ||||||||||||
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Title | Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (State I-C) | ||||||||||||
Map data | Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (State I-C) | ||||||||||||
Sample |
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Keywords | release factor 3 / termination complex / cryo-EM / tRNA / RIBOSOME | ||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Rybak MY / Li L / Lin J / Gagnon MG | ||||||||||||
Funding support | United States, China, 3 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: The ribosome termination complex remodels release factor RF3 and ejects GDP. Authors: Li Li / Mariia Yu Rybak / Jinzhong Lin / Matthieu G Gagnon / Abstract: Translation termination involves release factors RF1, RF2 and the GTPase RF3 that recycles RF1 and RF2 from the ribosome. RF3 dissociates from the ribosome in the GDP-bound form and must then ...Translation termination involves release factors RF1, RF2 and the GTPase RF3 that recycles RF1 and RF2 from the ribosome. RF3 dissociates from the ribosome in the GDP-bound form and must then exchange GDP for GTP. The 70S ribosome termination complex (70S-TC) accelerates GDP exchange in RF3, suggesting that the 70S-TC can function as the guanine nucleotide exchange factor for RF3. Here, we use cryogenic-electron microscopy to elucidate the mechanism of GDP dissociation from RF3 catalyzed by the Escherichia coli 70S-TC. The non-rotated ribosome bound to RF1 remodels RF3 and induces a peptide flip in the phosphate-binding loop, efficiently ejecting GDP. Binding of GTP allows RF3 to dock at the GTPase center, promoting the dissociation of RF1 from the ribosome. The structures recapitulate the functional cycle of RF3 on the ribosome and uncover the mechanism by which the 70S-TC allosterically dismantles the phosphate-binding groove in RF3, a previously overlooked function of the ribosome. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29622.map.gz | 255.8 MB | EMDB map data format | |
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Header (meta data) | emd-29622-v30.xml emd-29622.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
Images | emd_29622.png | 154 KB | ||
Masks | emd_29622_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-29622.cif.gz | 4.4 KB | ||
Others | emd_29622_additional_1.map.gz emd_29622_half_map_1.map.gz emd_29622_half_map_2.map.gz | 444.9 MB 474.9 MB 474.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29622 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29622 | HTTPS FTP |
-Validation report
Summary document | emd_29622_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_29622_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_29622_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | emd_29622_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29622 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29622 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29622.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (State I-C) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29622_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Cryo-EM structure of an E. coli rotated ribosome...
File | emd_29622_additional_1.map | ||||||||||||
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Annotation | Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (State I-C). Sharpened map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of an E. coli rotated ribosome...
File | emd_29622_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (State I-C). Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of an E. coli rotated ribosome...
File | emd_29622_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (State I-C). Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of an E. coli rotated ribosome complex bound wi...
Entire | Name: Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (State I-C) |
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Components |
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-Supramolecule #1: Cryo-EM structure of an E. coli rotated ribosome complex bound wi...
Supramolecule | Name: Cryo-EM structure of an E. coli rotated ribosome complex bound with RF3-ppGpp and p/E-tRNAPhe (State I-C) type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MRE600 |
Molecular weight | Theoretical: 2.6 MDa |
-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: 5 mM Tris-HCl, 60 mM NH4Cl, 10 mM MgCl2, 6 mM B-mercaptoethanol |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 10284 / Average exposure time: 1.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 96000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |