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Yorodumi- EMDB-15795: Translating 70S ribosome in the rotated state (A/P and P/E tRNAs) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15795 | |||||||||||||||
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Title | Translating 70S ribosome in the rotated state (A/P and P/E tRNAs) | |||||||||||||||
Map data | Post-processed (localfilter from cryoSPARC) map from Homogeneous Refinement | |||||||||||||||
Sample |
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Keywords | 70S / bacterial / translation / high-resolution / RIBOSOME | |||||||||||||||
Biological species | Escherichia coli B (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.1 Å | |||||||||||||||
Authors | Fromm SA / O'Connor KM / Purdy M / Bhatt PR / Loughran G / Atkins JF / Jomaa A / Mattei S | |||||||||||||||
Funding support | Ireland, European Union, 4 items
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Citation | Journal: Nat Commun / Year: 2023 Title: The translating bacterial ribosome at 1.55 Å resolution generated by cryo-EM imaging services. Authors: Simon A Fromm / Kate M O'Connor / Michael Purdy / Pramod R Bhatt / Gary Loughran / John F Atkins / Ahmad Jomaa / Simone Mattei / Abstract: Our understanding of protein synthesis has been conceptualised around the structure and function of the bacterial ribosome. This complex macromolecular machine is the target of important ...Our understanding of protein synthesis has been conceptualised around the structure and function of the bacterial ribosome. This complex macromolecular machine is the target of important antimicrobial drugs, an integral line of defence against infectious diseases. Here, we describe how open access to cryo-electron microscopy facilities combined with bespoke user support enabled structural determination of the translating ribosome from Escherichia coli at 1.55 Å resolution. The obtained structures allow for direct determination of the rRNA sequence to identify ribosome polymorphism sites in the E. coli strain used in this study and enable interpretation of the ribosomal active and peripheral sites at unprecedented resolution. This includes scarcely populated chimeric hybrid states of the ribosome engaged in several tRNA translocation steps resolved at ~2 Å resolution. The current map not only improves our understanding of protein synthesis but also allows for more precise structure-based drug design of antibiotics to tackle rising bacterial resistance. #1: Journal: Biorxiv / Year: 2022 Title: The translating bacterial ribosome at 1.55 angstrom resolution by open access cryo-EM Authors: Fromm SA / O'Connor KM / Purdy M / Bhatt PR / Loughran G / Atkins JF / Jomaa A / Mattei S | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15795.map.gz | 64.8 MB | EMDB map data format | |
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Header (meta data) | emd-15795-v30.xml emd-15795.xml | 26.8 KB 26.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15795_fsc.xml | 18.3 KB | Display | FSC data file |
Images | emd_15795.png | 100.6 KB | ||
Masks | emd_15795_msk_1.map | 669.9 MB | Mask map | |
Filedesc metadata | emd-15795.cif.gz | 5.1 KB | ||
Others | emd_15795_half_map_1.map.gz emd_15795_half_map_2.map.gz | 621.5 MB 621.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15795 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15795 | HTTPS FTP |
-Related 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_15795.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Post-processed (localfilter from cryoSPARC) map from Homogeneous Refinement | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.731 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15795_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_15795_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_15795_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 70S ribosome
Entire | Name: 70S ribosome |
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Components |
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-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#53 |
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Source (natural) | Organism: Escherichia coli B (bacteria) |
Molecular weight | Theoretical: 2.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.2 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Details: Fischione 1070 | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 19449 / Average exposure time: 5.2 sec. / Average electron dose: 40.0 e/Å2 Details: saved in EER format; 16 exposures per hole/stage movement. 11 in outer ring around the hole edge, 5 in inner ring around the hole center. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |