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Yorodumi- PDB-2df6: Crystal Structure of the SH3 Domain of betaPIX in Complex with a ... -
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-Basic information
Entry | Database: PDB / ID: 2df6 | ||||||
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Title | Crystal Structure of the SH3 Domain of betaPIX in Complex with a High Affinity Peptide from PAK2 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / SH3 domain / Peptide interaction | ||||||
Function / homology | Function and homology information CD28 dependent Vav1 pathway / negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / VEGFR2 mediated vascular permeability / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / CD209 (DC-SIGN) signaling / signal transduction => GO:0007165 / presynaptic actin cytoskeleton organization / VEGFA-VEGFR2 Pathway / small GTPase binding => GO:0031267 ...CD28 dependent Vav1 pathway / negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / VEGFR2 mediated vascular permeability / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / CD209 (DC-SIGN) signaling / signal transduction => GO:0007165 / presynaptic actin cytoskeleton organization / VEGFA-VEGFR2 Pathway / small GTPase binding => GO:0031267 / negative regulation of microtubule nucleation / Generation of second messenger molecules / Ephrin signaling / RHOU GTPase cycle / RHOV GTPase cycle / NRAGE signals death through JNK / EGFR downregulation / Smooth Muscle Contraction / G alpha (12/13) signalling events / MAPK6/MAPK4 signaling / RHOQ GTPase cycle / RAC1 GTPase cycle / RHOA GTPase cycle / FCERI mediated MAPK activation / protein localization to cell-cell junction / storage vacuole / astrocyte cell migration / positive regulation of growth hormone secretion / postsynaptic actin cytoskeleton organization / dendritic spine development / bicellular tight junction assembly / adherens junction assembly / gamma-tubulin binding / cardiac muscle hypertrophy / positive regulation of extrinsic apoptotic signaling pathway / stress-activated protein kinase signaling cascade / negative regulation of stress fiber assembly / lamellipodium assembly / small GTPase-mediated signal transduction / regulation of axonogenesis / activation of protein kinase activity / protein tyrosine kinase activator activity / mitotic spindle pole / regulation of cytoskeleton organization / Golgi organization / Rho protein signal transduction / cellular response to organic cyclic compound / GABA-ergic synapse / hematopoietic progenitor cell differentiation / cellular response to transforming growth factor beta stimulus / ruffle / phosphorylation / guanyl-nucleotide exchange factor activity / secretory granule / small GTPase binding / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell junction / lamellipodium / cell cortex / growth cone / peptidyl-serine phosphorylation / postsynapse / protein autophosphorylation / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / positive regulation of apoptotic process / protein phosphorylation / focal adhesion / protein serine/threonine kinase activity / centrosome / neuronal cell body / glutamatergic synapse / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / protein-containing complex / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Hoelz, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Crystal Structure of the SH3 Domain of betaPIX in Complex with a High Affinity Peptide from PAK2 Authors: Hoelz, A. / Janz, J.M. / Lawrie, S.D. / Corwin, B. / Lee, A. / Sakmar, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2df6.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2df6.ent.gz | 31.3 KB | Display | PDB format |
PDBx/mmJSON format | 2df6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/2df6 ftp://data.pdbj.org/pub/pdb/validation_reports/df/2df6 | HTTPS FTP |
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-Related structure data
Related structure data | 2g6fSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6731.333 Da / Num. of mol.: 2 / Fragment: SH3 domain(residues 10-63) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arhgef7, Pak3bp, Pixb / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O55043 #2: Protein/peptide | Mass: 2053.364 Da / Num. of mol.: 2 / Fragment: residues 180-197 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in human, rat. References: GenBank: 5138914, UniProt: Q64303*PLUS, EC: 2.7.1.37 #3: 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: 2.08 Å3/Da / Density % sol: 40.77 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 100mM MES, 35% PEG 5000MME, 200mM ammonium sulfate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.979191 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 7, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979191 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 35167 / Num. obs: 35167 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.3→1.32 Å / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2G6F Resolution: 1.3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.3→30 Å
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