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Yorodumi- EMDB-6585: The structure of elongation factor 4 (EF4/LepA) in GTP form bound... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6585 | |||||||||
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Title | The structure of elongation factor 4 (EF4/LepA) in GTP form bound to the ribosome | |||||||||
Map data | Reconstruction of EF4 bound to the 70S ribosome | |||||||||
Sample |
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Keywords | LepA / EF4 / ribosome / 70S | |||||||||
Function / homology | Function and homology information : / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / positive regulation of translation / large ribosomal subunit / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly ...: / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / positive regulation of translation / large ribosomal subunit / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 Å | |||||||||
Authors | Kumar V / Ahmed T / Ero R / Jian G-K / Yin Z / Gao Y / Bhushan S | |||||||||
Citation | Journal: J Biol Chem / Year: 2016 Title: Structure of the GTP Form of Elongation Factor 4 (EF4) Bound to the Ribosome. Authors: Veerendra Kumar / Rya Ero / Tofayel Ahmed / Kwok Jian Goh / Yin Zhan / Shashi Bhushan / Yong-Gui Gao / Abstract: Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase factors, along with elongation factor G and BPI-inducible protein A. Although EF4 is highly conserved in ...Elongation factor 4 (EF4) is a member of the family of ribosome-dependent translational GTPase factors, along with elongation factor G and BPI-inducible protein A. Although EF4 is highly conserved in bacterial, mitochondrial, and chloroplast genomes, its exact biological function remains controversial. Here we present the cryo-EM reconstitution of the GTP form of EF4 bound to the ribosome with P and E site tRNAs at 3.8-Å resolution. Interestingly, our structure reveals an unrotated ribosome rather than a clockwise-rotated ribosome, as observed in the presence of EF4-GDP and P site tRNA. In addition, we also observed a counterclockwise-rotated form of the above complex at 5.7-Å resolution. Taken together, our results shed light on the interactions formed between EF4, the ribosome, and the P site tRNA and illuminate the GTPase activation mechanism at previously unresolved detail. | |||||||||
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_6585.map.gz | 12.8 MB | EMDB map data format | |
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Header (meta data) | emd-6585-v30.xml emd-6585.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | 400_6585.gif 80_6585.gif | 71.9 KB 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6585 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6585 | HTTPS FTP |
-Validation report
Summary document | emd_6585_validation.pdf.gz | 331.7 KB | Display | EMDB validaton report |
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Full document | emd_6585_full_validation.pdf.gz | 331.3 KB | Display | |
Data in XML | emd_6585_validation.xml.gz | 6.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6585 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6585 | HTTPS FTP |
-Related structure data
Related structure data | 5imrMC 6584C 5imqC C: citing same article (ref.) M: atomic model generated by this map |
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Similar 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_6585.map.gz / Format: CCP4 / Size: 126.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of EF4 bound to the 70S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.28 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 : The structure of elongation factor 4 (EF4/LepA) in GTP form bound...
Entire | Name: The structure of elongation factor 4 (EF4/LepA) in GTP form bound to the ribosome |
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Components |
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-Supramolecule #1000: The structure of elongation factor 4 (EF4/LepA) in GTP form bound...
Supramolecule | Name: The structure of elongation factor 4 (EF4/LepA) in GTP form bound to the ribosome type: sample / ID: 1000 / Oligomeric state: 1 / Number unique components: 1 |
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Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.5 MDa / Method: Sedimentation |
-Supramolecule #1: Thermus thermophilus
Supramolecule | Name: Thermus thermophilus / type: complex / ID: 1 / Name.synonym: 70S ribosome / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Thermus thermophilus (bacteria) / Location in cell: Translation |
Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.5 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 5 mM HEPES, pH 7.5, 10 mM MgOAc, 50 mM KCl, 10 mM NH4Cl, 6 mM 2-mercaptoethanol |
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Grid | Details: 300 mesh copper grid with 2 nm carbon support, glow-discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 3 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 73684 times magnification |
Date | Jul 24, 2015 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 480 / Average electron dose: 20 e/Å2 Details: Every image is the average of seven frames recorded by the direct electron detector |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 109375 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 78000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Particles were selected using EMAN and processed using Relion |
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CTF correction | Details: Ctffind3 |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 18100 |