+Open data
-Basic information
Entry | Database: PDB / ID: 1g7c | ||||||
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Title | YEAST EEF1A:EEF1BA IN COMPLEX WITH GDPNP | ||||||
Components |
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Keywords | TRANSLATION / protein-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 / actin filament bundle assembly ...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 / actin filament bundle assembly / translational elongation / translation elongation factor activity / Neutrophil degranulation / cellular response to amino acid starvation / guanyl-nucleotide exchange factor activity / negative regulation of protein phosphorylation / negative regulation of protein kinase activity / maintenance of translational fidelity / 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: 2.05 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: to be published Title: Structural Basis for Nucleotide Exchange and Competition with tRNA in the Yeast Elongation Factor Complex eEF1A:eEF1Ba Authors: Andersen, G.R. / Pedersen, L. / Valente, L. / Kinzy, T.G. / Nyborg, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g7c.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g7c.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 1g7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/1g7c ftp://data.pdbj.org/pub/pdb/validation_reports/g7/1g7c | HTTPS FTP |
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-Related structure data
Related structure data | 1ijeC 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: 10472.829 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: TKY331 / Gene: TEF5 / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / Strain (production host): 834 DE3 / References: UniProt: P32471 |
#3: Chemical | ChemComp-5GP / |
#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: 2.19 Å3/Da / Density % sol: 43.93 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: mmE 2K, Tris, Hepes, KCl, DTT, GDPNP, 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: Sep 10, 2000 / Details: mirrors |
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: 2.05→20 Å / Num. all: 34086 / Num. obs: 33704 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 5.2 / % possible all: 93 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 93 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1f60 Resolution: 2.05→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: engh & huber
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Displacement parameters | Biso mean: 21.6 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.208 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.6 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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