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Yorodumi- PDB-6tkz: Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tkz | |||||||||
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Title | Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42 | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / guanine nucleotide exchange factor / cytoskeleton / actin / cryoEM | |||||||||
Function / homology | Function and homology information marginal zone B cell differentiation / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis ...marginal zone B cell differentiation / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / modulation by host of viral process / GTP-dependent protein binding / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / thioesterase binding / embryonic heart tube development / regulation of stress fiber assembly / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / positive regulation of filopodium assembly / regulation of postsynapse organization / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / heart contraction / Myogenesis / RHOJ GTPase cycle / RHOQ GTPase cycle / Golgi organization / positive regulation of cytokinesis / RHO GTPases activate PAKs / B cell homeostasis / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / RAC3 GTPase cycle / spindle midzone / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / phagocytic vesicle / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / secretory granule / positive regulation of DNA replication / filopodium / integrin-mediated signaling pathway / RHO GTPases Activate Formins / actin filament organization / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / EGFR downregulation / positive regulation of JNK cascade / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / protein localization / G beta:gamma signalling through CDC42 / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | |||||||||
Authors | Barford, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Biorxiv / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tkz.cif.gz | 312.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tkz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/6tkz ftp://data.pdbj.org/pub/pdb/validation_reports/tk/6tkz | HTTPS FTP |
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-Related structure data
Related structure data | 6tkyC 6tm1C 2wm9S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 53083.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DOCK10, KIAA0694, ZIZ3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q96BY6 #2: Protein | Mass: 20958.135 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P60953, small monomeric GTPase #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.49 Å3/Da / Density % sol: 50.54 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.5 Details: 25% (w/v) PEG 3350, 200 mM potassium acetate, 8% (v/v) 1,1,1,3,3,3-Hexafluoro-2-propanol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2009 |
Radiation | Monochromator: single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→82.48 Å / Num. obs: 45143 / % possible obs: 99.9 % / Redundancy: 7.76 % / Biso Wilson estimate: 48.63 Å2 / Rsym value: 0.114 / Net I/av σ(I): 6.47 / Net I/σ(I): 6.47 |
Reflection shell | Resolution: 2.6→2.74 Å / Num. unique obs: 6562 / Rsym value: 0.35 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WM9 Resolution: 2.64→82.48 Å / SU ML: 0.3341 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2778 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→82.48 Å
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Refine LS restraints |
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LS refinement shell |
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