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Yorodumi- EMDB-29630: RF3-GDPCP bound to an E. coli rotated ribosome, from focused clas... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29630 | ||||||||||||
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Title | RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-B) | ||||||||||||
Map data | RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-B) | ||||||||||||
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: 3.6 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 L / Rybak MY / Lin J / Gagnon MG | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29630.map.gz | 253.1 MB | EMDB map data format | |
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Header (meta data) | emd-29630-v30.xml emd-29630.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_29630.png | 75.2 KB | ||
Masks | emd_29630_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-29630.cif.gz | 4.6 KB | ||
Others | emd_29630_additional_1.map.gz emd_29630_half_map_1.map.gz emd_29630_half_map_2.map.gz | 433.5 MB 474.5 MB 474.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29630 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29630 | HTTPS FTP |
-Validation report
Summary document | emd_29630_validation.pdf.gz | 979.8 KB | Display | EMDB validaton report |
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Full document | emd_29630_full_validation.pdf.gz | 979.4 KB | Display | |
Data in XML | emd_29630_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_29630_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29630 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29630 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29630.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-B) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_29630_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: RF3-GDPCP bound to an E. coli rotated ribosome,...
File | emd_29630_additional_1.map | ||||||||||||
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Annotation | RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-B). Sharpened map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RF3-GDPCP bound to an E. coli rotated ribosome,...
File | emd_29630_half_map_1.map | ||||||||||||
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Annotation | RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-B). Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RF3-GDPCP bound to an E. coli rotated ribosome,...
File | emd_29630_half_map_2.map | ||||||||||||
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Annotation | RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-B). Half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : RF3-GDPCP bound to an E. coli rotated ribosome, from focused clas...
Entire | Name: RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-B) |
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Components |
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-Supramolecule #1: RF3-GDPCP bound to an E. coli rotated ribosome, from focused clas...
Supramolecule | Name: RF3-GDPCP bound to an E. coli rotated ribosome, from focused classification and refinement (State II-B) 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: 9810 / Average exposure time: 1.0 sec. / Average electron dose: 40.44 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 |