+Open data
-Basic information
Entry | Database: PDB / ID: 1aoj | ||||||
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Title | THE SH3 DOMAIN OF EPS8 EXISTS AS A NOVEL INTERTWINED DIMER | ||||||
Components | EPS8 | ||||||
Keywords | SIGNAL TRANSDUCTION / SH3 DOMAIN / EPS8 / PROLINE RICH PEPTIDE | ||||||
Function / homology | Function and homology information regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / stereocilium bundle / behavioral response to ethanol / stereocilium / exit from mitosis / regulation of Rho protein signal transduction ...regulation of actin filament length / actin polymerization-dependent cell motility / dendritic cell migration / stereocilium tip / actin crosslink formation / stereocilium bundle / behavioral response to ethanol / stereocilium / exit from mitosis / regulation of Rho protein signal transduction / barbed-end actin filament capping / NMDA selective glutamate receptor complex / positive regulation of ruffle assembly / Rac protein signal transduction / regulation of postsynaptic membrane neurotransmitter receptor levels / actin filament bundle assembly / brush border / Rho protein signal transduction / cellular response to leukemia inhibitory factor / adult locomotory behavior / ruffle membrane / small GTPase binding / actin binding / cell cortex / regulation of cell shape / growth cone / actin cytoskeleton organization / postsynaptic density / glutamatergic synapse / synapse / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kishan, K.V.R. / Newcomer, M.E. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: The SH3 domain of Eps8 exists as a novel intertwined dimer. Authors: Kishan, K.V. / Scita, G. / Wong, W.T. / Di Fiore, P.P. / Newcomer, M.E. #1: Journal: Embo J. / Year: 1993 Title: Eps8, a Substrate for the Epidermal Growth Factor Receptor Kinase, Enhances Egf-Dependent Mitogenic Signals Authors: Fazioli, F. / Minichiello, L. / Matoska, V. / Castagnino, P. / Miki, T. / Wong, W.T. / Di Fiore, P.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aoj.cif.gz | 33.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aoj.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 1aoj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/1aoj ftp://data.pdbj.org/pub/pdb/validation_reports/ao/1aoj | HTTPS FTP |
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-Related structure data
Related structure data | 1shfS S: Starting model for refinement |
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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: 7044.960 Da / Num. of mol.: 2 / Fragment: SH3 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q08509 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.52 % | |||||||||||||||
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 0.4M SODIUM POTASSIUM TARTRATE, PH 7.5. PROTEIN CONC. 6MG/ML. CRYSTALLIZATION TIME 2-3 WEEKS. | |||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1996 / Details: MSC/YALE MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→32 Å / Num. obs: 3406 / % possible obs: 97 % / Observed criterion σ(I): 4 / Redundancy: 6.2 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 3.3 / % possible all: 92 |
Reflection | *PLUS Num. measured all: 21281 |
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SHF Resolution: 2.5→32 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: R-FREE THROUGHOUT / σ(F): 2 / Stereochemistry target values: TNT PROTGEO Details: REFINEMENT FIRST STARTED WITH X-PLOR SIMULATED ANNEALING PROTOCOL
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Solvent computation | Bsol: 192 Å2 / ksol: 0.679 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→32 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.193 / Rfactor Rfree: 0.277 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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