+Open data
-Basic information
Entry | Database: PDB / ID: 1ije | ||||||
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Title | Nucleotide Exchange Intermediates in the eEF1A-eEF1Ba Complex | ||||||
Components |
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Keywords | TRANSLATION / protein complex | ||||||
Function / homology | Function and homology information Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / negative regulation of actin filament bundle assembly / HSF1 activation / melatonin binding / regulation of translational termination / tRNA export from nucleus / Protein methylation / fungal-type vacuole membrane / translational elongation ...Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / negative regulation of actin filament bundle assembly / HSF1 activation / melatonin binding / regulation of translational termination / tRNA export from nucleus / Protein methylation / fungal-type vacuole membrane / translational elongation / actin filament bundle assembly / translation elongation factor activity / Neutrophil degranulation / cellular response to amino acid starvation / guanyl-nucleotide exchange factor activity / negative regulation of protein phosphorylation / maintenance of translational fidelity / negative regulation of protein kinase activity / GDP binding / actin filament binding / ribosome binding / cytoskeleton / ribosome / translation / GTPase activity / GTP binding / protein kinase binding / mitochondrion / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Andersen, G.R. / Valente, L. / Pedersen, L. / Kinzy, T.G. / Nyborg, J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Crystal structures of nucleotide exchange intermediates in the eEF1A-eEF1Balpha complex. Authors: Andersen, G.R. / Valente, L. / Pedersen, L. / Kinzy, T.G. / Nyborg, J. #1: Journal: Mol.Cell / Year: 2000 Title: Structural basis for nucleotide exchange and competition with tRNA in the yeast elongation factor complex eEF1A:eEF1Balpha Authors: Andersen, G.R. / Pedersen, L. / Valente, L. / Chatterjee, I.I. / Kinzy, T.G. / Kjeldgaard, M. / Nyborg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ije.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ije.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ije.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/1ije ftp://data.pdbj.org/pub/pdb/validation_reports/ij/1ije | HTTPS FTP |
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-Related structure data
Related structure data | 1g7cC 1ijfC 1f60S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50110.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02994 |
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#2: Protein | Mass: 10046.277 Da / Num. of mol.: 1 / Fragment: catalytical C-terminal fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TEF5 / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): 834 DE3 / References: UniProt: P32471 |
#3: Chemical | ChemComp-GDP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.35 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: mmE2K, Tris, Hepes, KCl, DTT, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 Details: Pedersen, L.P., (2000) Acta Crystallogr., D57, 159. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 13, 2001 / Details: graphite monochromator |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 21448 / Num. obs: 21223 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.205 / Num. unique all: 2110 |
Reflection | *PLUS Lowest resolution: 20 Å / % possible obs: 100 % |
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 99 % / Mean I/σ(I) obs: 6.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1f60 Resolution: 2.4→19.88 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 346790.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.68 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.4 % / Rfactor Rfree: 0.25 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.276 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.228 |