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Yorodumi- EMDB-1233: Structure of eEF3 and the mechanism of transfer RNA release from ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1233 | |||||||||
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Title | Structure of eEF3 and the mechanism of transfer RNA release from the E-site. | |||||||||
Map data | Cryo-EM density map of yeast eEF3 bound to translating yeast 80S ribosome | |||||||||
Sample |
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Function / homology | Function and homology information translational elongation / translation elongation factor activity / translational termination / cytosolic ribosome / negative regulation of protein phosphorylation / negative regulation of protein kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / ribosome binding / rRNA binding ...translational elongation / translation elongation factor activity / translational termination / cytosolic ribosome / negative regulation of protein phosphorylation / negative regulation of protein kinase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / ribosome binding / rRNA binding / ribosome / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 9.9 Å | |||||||||
Authors | Beckmann R / Andersen G | |||||||||
Citation | Journal: Nature / Year: 2006 Title: Structure of eEF3 and the mechanism of transfer RNA release from the E-site. Authors: Christian B F Andersen / Thomas Becker / Michael Blau / Monika Anand / Mario Halic / Bharvi Balar / Thorsten Mielke / Thomas Boesen / Jan Skov Pedersen / Christian M T Spahn / Terri Goss ...Authors: Christian B F Andersen / Thomas Becker / Michael Blau / Monika Anand / Mario Halic / Bharvi Balar / Thorsten Mielke / Thomas Boesen / Jan Skov Pedersen / Christian M T Spahn / Terri Goss Kinzy / Gregers R Andersen / Roland Beckmann / Abstract: Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of ...Elongation factor eEF3 is an ATPase that, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of the aminoacyl-tRNA-eEF1A-GTP ternary complex to the ribosomal A-site and has been suggested to facilitate the clearance of deacyl-tRNA from the E-site. Here we present the crystal structure of Saccharomyces cerevisiae eEF3, showing that it consists of an amino-terminal HEAT repeat domain, followed by a four-helix bundle and two ABC-type ATPase domains, with a chromodomain inserted in ABC2. Moreover, we present the cryo-electron microscopy structure of the ATP-bound form of eEF3 in complex with the post-translocational-state 80S ribosome from yeast. eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain likely to stabilize the ribosomal L1 stalk in an open conformation, thus allowing tRNA release. | |||||||||
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_1233.map.gz | 73.8 MB | EMDB map data format | |
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Header (meta data) | emd-1233-v30.xml emd-1233.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | 1233.gif | 18.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1233 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1233 | HTTPS FTP |
-Validation report
Summary document | emd_1233_validation.pdf.gz | 286.9 KB | Display | EMDB validaton report |
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Full document | emd_1233_full_validation.pdf.gz | 286 KB | Display | |
Data in XML | emd_1233_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1233 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1233 | HTTPS FTP |
-Related structure data
Related structure data | 2ix8MC 2iw3C 2iwhC 2ix3C 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_1233.map.gz / Format: CCP4 / Size: 78.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM density map of yeast eEF3 bound to translating yeast 80S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size |
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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-RNC-eEF3-AMP-PNP complex from S. cerevisiae
Entire | Name: 80S-RNC-eEF3-AMP-PNP complex from S. cerevisiae |
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Components |
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-Supramolecule #1000: 80S-RNC-eEF3-AMP-PNP complex from S. cerevisiae
Supramolecule | Name: 80S-RNC-eEF3-AMP-PNP complex from S. cerevisiae / type: sample / ID: 1000 Details: The emerging signal sequence of the ribosome nascent chain (RNC) was saturated using purified trimeric Sec61 complex in order to prevent biased orientation of particles Oligomeric state: One ribosome binds to one molecule of eEF3 Number unique components: 2 |
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Molecular weight | Theoretical: 4.3 MDa |
-Supramolecule #1: programmed 80S ribosome
Supramolecule | Name: programmed 80S ribosome / type: complex / ID: 1 / Name.synonym: RNC / Details: programmed 80S ribosome with a P-site tRNA / Ribosome-details: ribosome-eukaryote: ALL |
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Molecular weight | Experimental: 4.2 MDa / Theoretical: 4.2 MDa |
-Macromolecule #1: elongation factor 3
Macromolecule | Name: elongation factor 3 / type: protein_or_peptide / ID: 1 / Name.synonym: eEF3 / Details: eEF3 with a C-terminal His-Tag and a factor / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Saccharomyces Cerevisiae / Cell: Saccharomyces Cerevisiae / Organelle: cytosol / Location in cell: cytosol |
Molecular weight | Experimental: 115 KDa / Theoretical: 115 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: pYES2.1 TOPO |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.168 mg/mL |
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Buffer | pH: 7.5 Details: 20 mM HEPES, pH 7.5, 10 mM Mg(OAc)2, 150 mM KOAc 1 mM DTT, 0.05% Nikkol, 125 mM Sucrose,0.01 mg ml-1 Cycloheximide, 0.5 mM AMP-PNP, 0.1 mM Neomycin, 0.3 % DesoxyBigChaps |
Staining | Type: NEGATIVE / Details: Cryo-EM, no staining |
Grid | Details: Quantifoil grids 200 mesh R2/4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot Method: Blot for 10 seconds before plunging, use 2 layers of filter paper |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Min: 95 K / Average: 95 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 100,000 time |
Date | Jan 13, 2005 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 4.35 µm / Number real images: 141 / Average electron dose: 20 e/Å2 / Od range: 1.2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 38900 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.27 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: Polara Multispecimen Holder / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 37700 |
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-Atomic model buiding 1
Software | Name: O and Situs |
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Details | Protocol: rigid body. The domains were separately fitted by manual docking using program O |
Refinement | Protocol: RIGID BODY FIT / Target criteria: cross correlation |
Output model | PDB-2ix8: |