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Yorodumi- PDB-2b7b: Yeast guanine nucleotide exchange factor eEF1Balpha K205A mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b7b | ||||||
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Title | Yeast guanine nucleotide exchange factor eEF1Balpha K205A mutant in complex with eEF1A and GDP | ||||||
Components |
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Keywords | TRANSLATION / G-protein-GEF complex / eEF1A / eEF1Balpha | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Pittman, Y.R. / Valente, L. / Jeppesen, M.G. / Andersen, G.R. / Patel, S. / Kinzy, T.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Mg2+ and a key lysine modulate exchange activity of eukaryotic translation elongation factor 1B alpha Authors: Pittman, Y.R. / Valente, L. / Jeppesen, M.G. / Andersen, G.R. / Patel, S. / Kinzy, T.G. #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. / Kinzy, T.G. / Kjeldgaard, M. / Nyborg, J. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b7b.cif.gz | 123.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b7b.ent.gz | 92.3 KB | Display | PDB format |
PDBx/mmJSON format | 2b7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/2b7b ftp://data.pdbj.org/pub/pdb/validation_reports/b7/2b7b | HTTPS FTP |
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-Related structure data
Related structure data | 2b7cC 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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Details | The biological unit consists of one molecule each of eF1A and eEF1Balpha |
-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: 10414.727 Da / Num. of mol.: 1 / Fragment: C-terminal domain / Mutation: K1205A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TEF5 / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32471 | ||
#3: Chemical | #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: 2.23 Å3/Da / Density % sol: 44.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 12% PEG 2000 MME, 100mM Tris-Cl pH 7.6, 100mM KCl, 3mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9798 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 9, 2002 / Details: Three-segment Pt-coated toroidal mirrors |
Radiation | Monochromator: Double Crystal (Si111, Si220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. all: 17083 / Num. obs: 17083 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 1.4 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PBD entry 1F60 Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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