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Yorodumi- EMDB-5017: Segmented eEF2 density from the cryo-EM map of eEF2-bound 80S complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5017 | |||||||||
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Title | Segmented eEF2 density from the cryo-EM map of eEF2-bound 80S complex | |||||||||
Map data | Segmented eEF2 density from the 80S.eEF2 cryo-EM map | |||||||||
Sample |
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Keywords | AlF4- / GDP / GTPase / Ribosome / Translocation | |||||||||
Function / homology | Function and homology information Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / maintenance of translational fidelity / ribosome binding ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / translational elongation / translation elongation factor activity / Neutrophil degranulation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / maintenance of translational fidelity / ribosome binding / protein-folding chaperone binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Thermomyces lanuginosus (fungus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.6 Å | |||||||||
Authors | Sengupta J / Nilsson J / Gursky R / Kjeldgaard M / Nissen P / Frank J | |||||||||
Citation | Journal: J Mol Biol / Year: 2008 Title: Visualization of the eEF2-80S ribosome transition-state complex by cryo-electron microscopy. Authors: Jayati Sengupta / Jakob Nilsson / Richard Gursky / Morten Kjeldgaard / Poul Nissen / Joachim Frank / Abstract: In an attempt to understand ribosome-induced GTP hydrolysis on eEF2, we determined a 12.6-A cryo-electron microscopy reconstruction of the eEF2-bound 80S ribosome in the presence of aluminum ...In an attempt to understand ribosome-induced GTP hydrolysis on eEF2, we determined a 12.6-A cryo-electron microscopy reconstruction of the eEF2-bound 80S ribosome in the presence of aluminum tetrafluoride and GDP, with aluminum tetrafluoride mimicking the gamma-phosphate during hydrolysis. This is the first visualization of a structure representing a transition-state complex on the ribosome. Tight interactions are observed between the factor's G domain and the large ribosomal subunit, as well as between domain IV and an intersubunit bridge. In contrast, some of the domains of eEF2 implicated in small subunit binding display a large degree of flexibility. Furthermore, we find support for a transition-state model conformation of the switch I region in this complex where the reoriented switch I region interacts with a conserved rRNA region of the 40S subunit formed by loops of the 18S RNA helices 8 and 14. This complex is structurally distinct from the eEF2-bound 80S ribosome complexes previously reported, and analysis of this map sheds light on the GTPase-coupled translocation mechanism. | |||||||||
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_5017.map.gz | 7.8 MB | EMDB map data format | |
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Header (meta data) | emd-5017-v30.xml emd-5017.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_5017_1.png | 105.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5017 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5017 | HTTPS FTP |
-Validation report
Summary document | emd_5017_validation.pdf.gz | 276.4 KB | Display | EMDB validaton report |
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Full document | emd_5017_full_validation.pdf.gz | 275.9 KB | Display | |
Data in XML | emd_5017_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5017 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5017 | HTTPS FTP |
-Related structure data
Related structure data | 3dnyMC 3dwuMC 5015C 5016C M: atomic model generated by this map C: citing same article (ref.) |
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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_5017.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Segmented eEF2 density from the 80S.eEF2 cryo-EM map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.82 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 : 80S.eEF2.AlF4.GDP
Entire | Name: 80S.eEF2.AlF4.GDP |
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Components |
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-Supramolecule #1000: 80S.eEF2.AlF4.GDP
Supramolecule | Name: 80S.eEF2.AlF4.GDP / type: sample / ID: 1000 Details: GDP-AlF4- traps ribosome-bound eEF2 in a transition state of GTP hydrolysis Number unique components: 4 |
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-Supramolecule #1: 80S ribosome
Supramolecule | Name: 80S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Thermomyces lanuginosus (fungus) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 / Details: 20 mM Hepes-NH3, 100 mM KCl, 20 mM MgCl2 |
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Grid | Details: Quantifoil grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: OTHER / Details: Vitrification instrument: vitrobot |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Category: CCD / Film or detector model: KODAK SO-163 FILM / Digitization - Sampling interval: 2.82 µm / Average electron dose: 10 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Single tilt cryo-holder / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Segregation in defocus groups and correction in volumes |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Details: Supervised Classification was used / Number images used: 1 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | Protocol: Rigid Body. The domains were separately fitted by manual docking using program O |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient |
Output model | PDB-3dny: PDB-3dwu: |