+Open data
-Basic information
Entry | Database: PDB / ID: 1gcp | ||||||
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Title | CRYSTAL STRUCTURE OF VAV SH3 DOMAIN | ||||||
Components | VAV PROTO-ONCOGENE | ||||||
Keywords | SIGNALING PROTEIN / SH3 DOMAIN / VAV | ||||||
Function / homology | Function and homology information Azathioprine ADME / CD28 dependent Vav1 pathway / RAC2 GTPase cycle / Erythropoietin activates RAS / GPVI-mediated activation cascade / FCERI mediated MAPK activation / RHOA GTPase cycle / NRAGE signals death through JNK / Signaling by SCF-KIT / RAC1 GTPase cycle ...Azathioprine ADME / CD28 dependent Vav1 pathway / RAC2 GTPase cycle / Erythropoietin activates RAS / GPVI-mediated activation cascade / FCERI mediated MAPK activation / RHOA GTPase cycle / NRAGE signals death through JNK / Signaling by SCF-KIT / RAC1 GTPase cycle / VEGFR2 mediated vascular permeability / RHOG GTPase cycle / FCERI mediated Ca+2 mobilization / phosphorylation-dependent protein binding / G alpha (12/13) signalling events / 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 / Interleukin-3, Interleukin-5 and GM-CSF signaling / VEGFA-VEGFR2 Pathway / positive regulation of natural killer cell mediated cytotoxicity / regulation of cell size / T cell differentiation / positive regulation of cell adhesion / phagocytosis / reactive oxygen species metabolic process / phosphotyrosine residue binding / T cell activation / neutrophil chemotaxis / guanyl-nucleotide exchange factor activity / integrin-mediated signaling pathway / cell migration / cell-cell junction / intracellular signal transduction / immune response / G protein-coupled receptor signaling pathway / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Nishida, M. / Nagata, K. / Hachimori, Y. / Ogura, K. / Inagaki, F. | ||||||
Citation | Journal: EMBO J. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gcp.cif.gz | 67.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gcp.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gcp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/1gcp ftp://data.pdbj.org/pub/pdb/validation_reports/gc/1gcp | HTTPS FTP |
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-Related structure data
Related structure data | 1gcqSC 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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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.) Mus musculus (house mouse) / Cell line: HEMATOPOIETIC CELLS / Plasmid: PET28A(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P27870 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: molecular replacement 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: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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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