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Open data
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Basic information
Entry | Database: PDB / ID: 1ijf | ||||||
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Title | Nucleotide exchange mechanisms in the eEF1A-eEF1Ba complex | ||||||
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![]() | TRANSLATION / protein complex | ||||||
Function / homology | ![]() 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 / sulfur compound metabolic process / Protein methylation / fungal-type vacuole membrane ...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 / sulfur compound metabolic process / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Andersen, G.R. / Valente, L. / Pedersen, L. / Kinzy, T.G. / Nyborg, J. | ||||||
![]() | ![]() 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: ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.3 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 772.7 KB | Display | ![]() |
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Full document | ![]() | 777.3 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g7cC ![]() 1ijeC ![]() 1f60S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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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.) ![]() ![]() Gene: TEF5 / Plasmid: pET11d / Production host: ![]() ![]() |
#3: Chemical | ChemComp-GDP / |
#4: Chemical | ChemComp-MG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 13, 2000 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→14 Å / Num. all: 11251 / Num. obs: 10905 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.172 / % possible all: 91 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 14 Å |
Reflection shell | *PLUS % possible obs: 91 % / Mean I/σ(I) obs: 5.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1f60 Resolution: 3→13.99 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 133306.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh and Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.296 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→13.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.042 / 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 % reflection Rfree: 5.3 % / Rfactor obs: 0.25 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.25 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.388 / % reflection Rfree: 5.6 % / Rfactor Rwork: 0.335 |