+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6474 | |||||||||
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Title | Cryo-EM structure of PoTC-EF-G(S588P)-GDPNP | |||||||||
Map data | Reconstruction of PoTC-EF-G(S588P)-GDPNP | |||||||||
Sample |
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Keywords | ribosome recycling / PoTC / EF-G / RRF / cryo-EM | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||
Authors | Zhang D / Yan K / Zhang Y / Liu G / Cao X / Song G / Xie Q / Gao N / Qin Y | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2015 Title: New insights into the enzymatic role of EF-G in ribosome recycling. Authors: Dejiu Zhang / Kaige Yan / Yiwei Zhang / Guangqiao Liu / Xintao Cao / Guangtao Song / Qiang Xie / Ning Gao / Yan Qin / Abstract: During translation, elongation factor G (EF-G) plays a catalytic role in tRNA translocation and a facilitative role in ribosome recycling. By stabilizing the rotated ribosome and interacting with ...During translation, elongation factor G (EF-G) plays a catalytic role in tRNA translocation and a facilitative role in ribosome recycling. By stabilizing the rotated ribosome and interacting with ribosome recycling factor (RRF), EF-G was hypothesized to induce the domain rotations of RRF, which subsequently performs the function of splitting the major intersubunit bridges and thus separates the ribosome into subunits for recycling. Here, with systematic mutagenesis, FRET analysis and cryo-EM single particle approach, we analyzed the interplay between EF-G/RRF and post termination complex (PoTC). Our data reveal that the two conserved loops (loop I and II) at the tip region of EF-G domain IV possess distinct roles in tRNA translocation and ribosome recycling. Specifically, loop II might be directly involved in disrupting the main intersubunit bridge B2a between helix 44 (h44 from the 30S subunit) and helix 69 (H69 from the 50S subunit) in PoTC. Therefore, our data suggest a new ribosome recycling mechanism which requires an active involvement of EF-G. In addition to supporting RRF, EF-G plays an enzymatic role in destabilizing B2a via its loop II. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6474.map.gz | 14.4 MB | EMDB map data format | |
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Header (meta data) | emd-6474-v30.xml emd-6474.xml | 7.5 KB 7.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6474_fsc.xml | 11 KB | Display | FSC data file |
Images | emd_6474.tif | 122.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6474 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6474 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6474.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of PoTC-EF-G(S588P)-GDPNP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : EF-G (S588P)-GDPNP bound to PoTC
Entire | Name: EF-G (S588P)-GDPNP bound to PoTC |
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Components |
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-Supramolecule #1000: EF-G (S588P)-GDPNP bound to PoTC
Supramolecule | Name: EF-G (S588P)-GDPNP bound to PoTC / type: sample / ID: 1000 / Number unique components: 2 |
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-Supramolecule #1: PoTC 70S ribosome
Supramolecule | Name: PoTC 70S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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-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 / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Date | Aug 16, 2015 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |