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Open data
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Basic information
Entry | Database: PDB / ID: 1gcp | ||||||
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Title | CRYSTAL STRUCTURE OF VAV SH3 DOMAIN | ||||||
![]() | VAV PROTO-ONCOGENE | ||||||
![]() | SIGNALING PROTEIN / SH3 DOMAIN / VAV | ||||||
Function / homology | ![]() Azathioprine ADME / CD28 dependent Vav1 pathway / Erythropoietin activates RAS / RAC2 GTPase cycle / GPVI-mediated activation cascade / FCERI mediated MAPK activation / NRAGE signals death through JNK / Signaling by SCF-KIT / RAC1 GTPase cycle / VEGFR2 mediated vascular permeability ...Azathioprine ADME / CD28 dependent Vav1 pathway / Erythropoietin activates RAS / RAC2 GTPase cycle / GPVI-mediated activation cascade / FCERI mediated MAPK activation / NRAGE signals death through JNK / Signaling by SCF-KIT / RAC1 GTPase cycle / VEGFR2 mediated vascular permeability / RHOA GTPase cycle / RHOG GTPase cycle / FCERI mediated Ca+2 mobilization / G alpha (12/13) signalling events / phosphorylation-dependent protein binding / PIP3 activates AKT signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of signaling by CBL / Regulation of actin dynamics for phagocytic cup formation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of natural killer cell mediated cytotoxicity / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / regulation of cell size / positive regulation of cell adhesion / T cell differentiation / phagocytosis / T cell activation / neutrophil chemotaxis / phosphotyrosine residue binding / reactive oxygen species metabolic process / guanyl-nucleotide exchange factor activity / integrin-mediated signaling pathway / cell-cell junction / cell migration / intracellular signal transduction / immune response / G protein-coupled receptor signaling pathway / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nishida, M. / Nagata, K. / Hachimori, Y. / Ogura, K. / Inagaki, F. | ||||||
![]() | ![]() Title: Novel recognition mode between Vav and Grb2 SH3 domains. Authors: Nishida, M. / Nagata, K. / Hachimori, Y. / Horiuchi, M. / Ogura, K. / Mandiyan, V. / Schlessinger, J. / Inagaki, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.5 KB | Display | ![]() |
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PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gcqSC 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8029.990 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.1 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 277.2 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG4000, tris(hydroxymethyl)aminomethane, isopropanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→8 Å / Num. all: 14004 / Num. obs: 14004 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Num. unique all: 1048 / % possible all: 70.7 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 84381 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Vav SH3 domain in 1GCQ Resolution: 2.1→8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 12 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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