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- PDB-6tm1: Crystal structure of the DHR2 domain of DOCK10 in complex with RAC3 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tm1 | ||||||
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Title | Crystal structure of the DHR2 domain of DOCK10 in complex with RAC3 | ||||||
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![]() | SIGNALING PROTEIN / DOCK10 GEF RAC3 GTPase | ||||||
Function / homology | ![]() cerebral cortex GABAergic interneuron development / postsynaptic actin cytoskeleton organization / marginal zone B cell differentiation / regulation of neuron maturation / regulation of neutrophil migration / NADPH oxidase complex / respiratory burst / cortical cytoskeleton organization / regulation of Rho protein signal transduction / dendritic spine morphogenesis ...cerebral cortex GABAergic interneuron development / postsynaptic actin cytoskeleton organization / marginal zone B cell differentiation / regulation of neuron maturation / regulation of neutrophil migration / NADPH oxidase complex / respiratory burst / cortical cytoskeleton organization / regulation of Rho protein signal transduction / dendritic spine morphogenesis / cell projection assembly / motor neuron axon guidance / PCP/CE pathway / positive regulation of cell adhesion mediated by integrin / synaptic transmission, GABAergic / small GTPase-mediated signal transduction / establishment or maintenance of cell polarity / Rac protein signal transduction / filamentous actin / B cell homeostasis / neuromuscular process controlling balance / CDC42 GTPase cycle / regulation of postsynapse assembly / RAC2 GTPase cycle / RAC3 GTPase cycle / homeostasis of number of cells within a tissue / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of GTPase activity / endomembrane system / regulation of cell migration / guanyl-nucleotide exchange factor activity / small monomeric GTPase / actin filament organization / cell periphery / cell chemotaxis / regulation of actin cytoskeleton organization / small GTPase binding / Wnt signaling pathway / calcium-dependent protein binding / lamellipodium / regulation of cell shape / G protein activity / Factors involved in megakaryocyte development and platelet production / actin cytoskeleton organization / growth cone / cytoplasmic vesicle / dendritic spine / cytoskeleton / postsynapse / neuron projection / intracellular signal transduction / neuronal cell body / GTPase activity / endoplasmic reticulum membrane / protein kinase binding / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barford, D. / Fan, D. / Cronin, N. / Yang, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for CDC42 and RAC activation by the dual specificity GEF DOCK10 Authors: Fan, D. / Yang, J. / Cronin, N. / Barford, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 234.1 KB | Display | ![]() |
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PDB format | ![]() | 144.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tkyC ![]() 6tkzC ![]() 2c2hS ![]() 2wm9S 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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Unit cell |
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Components
#1: Protein | Mass: 53026.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ...Details: STPELRRTWLESMAKIHARNGDLSEAAMCYIHIAALIAEYLKRKGYWKVEKICTASLLSEDTHPCDSNSLLTTPSGGSMFSMGWPAFLSITPNIKEEGAMKEDSGMQDTPYNENILVEQLYMCVEFLWKSERYELIADVNKPIIAVFEKQRDFKKLSDLYYDIHRSYLKVAEVVNSEKRLFGRYYRVAFYGQGFFEE EEGKEYIYKEPKLTGLSEISQRLLKLYADKFGADNVKIIQDSNKVNPKDLDPKYAYIQVTYVTPFFEEKEIEDRKTDFEMHHNINRFVFETPFTLSGKKH GGVAEQCKRRTILTTSHLFPYVKKRIQVISQSSTELNPIEVAIDEMSKKVSELNQLCTMEEVDMIRLQLKLQGSVSVKVNAGPMAYARAFLEETNAKKYP DNQVKLLKEIFRQFADACGQ ALDVNERLIK EDQLEYQEEL RSHYKDMLSE LSTVMNEQIT Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 21405.861 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 53083.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.75 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.5 Details: 25% (w/v) PEG 1500, 100 mM MMT. MMT buffer is produced by mixing DL-malic acid, MES and Tris base in the molar ratios of 1:2:2. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.71→29.6 Å / Num. obs: 29674 / % possible obs: 95.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 151.85 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.61 |
Reflection shell | Resolution: 3.71→3.85 Å / Rmerge(I) obs: 0.3 / Num. unique obs: 1515 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WM9,2C2H Resolution: 3.71→29.6 Å / SU ML: 0.6511 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 38.1002 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 148.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.71→29.6 Å
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Refine LS restraints |
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LS refinement shell |
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