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- PDB-5fi1: Crystal Structure of the P-Rex1 DH/PH tandem in complex with Cdc42 -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fi1 | ||||||||||||
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Title | Crystal Structure of the P-Rex1 DH/PH tandem in complex with Cdc42 | ||||||||||||
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![]() | SIGNALING PROTEIN / dbl homology domain / pleckstrin homology domain / GTPase / RhoGEF / PROTEIN BINDING | ||||||||||||
Function / homology | ![]() regulation of signaling / 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 ...regulation of signaling / 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 / regulation of dendrite development / 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 / cardiac conduction system development / Inactivation of CDC42 and RAC1 / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / regulation of actin filament polymerization / 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 / neutrophil activation / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / adherens junction organization / regulation of small GTPase mediated signal transduction / sprouting angiogenesis / DCC mediated attractive signaling / 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 / RHOV GTPase cycle / establishment or maintenance of cell polarity / RHOB GTPase cycle / phagocytosis, engulfment / superoxide metabolic process / heart contraction / NRAGE signals death through JNK / Myogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / positive regulation of cytokinesis / Golgi organization / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / T cell differentiation / RHOG GTPase cycle / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / phagocytic vesicle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / actin filament polymerization / neutrophil chemotaxis / GTPase activator activity / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / dendritic shaft / positive regulation of DNA replication / secretory granule / filopodium / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Cash, J.N. / Tesmer, J.J.G. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Biochemical Characterization of the Catalytic Core of the Metastatic Factor P-Rex1 and Its Regulation by PtdIns(3,4,5)P3. Authors: Cash, J.N. / Davis, E.M. / Tesmer, J.J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228.1 KB | Display | ![]() |
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PDB format | ![]() | 183.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.2 KB | Display | ![]() |
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Full document | ![]() | 434.3 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d27C ![]() 5d3vC ![]() 5d3wSC ![]() 5d3xC ![]() 5d3yC ![]() 5fi0C ![]() 2dfkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 43066.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: dbl homology domain/pleckstrin homology domain tandem Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 21616.922 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: 3.46 Å3/Da / Density % sol: 64.42 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Ammonium citrate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 20, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.16→50 Å / Num. obs: 12403 / % possible obs: 83.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 83.61 Å2 / Rmerge(I) obs: 0.071 / Χ2: 1.096 / Net I/av σ(I): 16.062 / Net I/σ(I): 8.3 / Num. measured all: 43371 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DFK, 5D3W Resolution: 3.203→43.122 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.79 / Stereochemistry target values: ML
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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 max: 252.6 Å2 / Biso mean: 124.726 Å2 / Biso min: 61.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.203→43.122 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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