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Yorodumi- PDB-5fi1: Crystal Structure of the P-Rex1 DH/PH tandem in complex with Cdc42 -
+Open data
-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 | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / dbl homology domain / pleckstrin homology domain / GTPase / RhoGEF / PROTEIN BINDING | ||||||||||||
Function / homology | Function and homology information 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 / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / neuron fate determination / modulation by host of viral process / 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 / neutrophil activation / GTP-dependent protein binding / 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 / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / embryonic heart tube development / thioesterase binding / 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 / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / regulation of mitotic nuclear division / establishment or maintenance of cell polarity / phagocytosis, engulfment / RHOV GTPase cycle / RHOB GTPase cycle / NRAGE signals death through JNK / superoxide metabolic process / heart contraction / Myogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / T cell differentiation / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / negative regulation of protein-containing complex assembly / phagocytic vesicle / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / actin filament polymerization / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / guanyl-nucleotide exchange factor activity / neutrophil chemotaxis / small monomeric GTPase / G protein activity / dendritic shaft / filopodium / positive regulation of DNA replication / secretory granule / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.203 Å | ||||||||||||
Authors | Cash, J.N. / Tesmer, J.J.G. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Structure / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fi1.cif.gz | 228.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fi1.ent.gz | 183.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/5fi1 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/5fi1 | HTTPS FTP |
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-Related structure data
Related structure data | 5d27C 5d3vC 5d3wSC 5d3xC 5d3yC 5fi0C 2dfkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: PREX1, KIAA1415 / Plasmid: pMALc2H10T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TCU6 |
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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.) Homo sapiens (human) / Gene: CDC42 / Plasmid: pMALc2H10T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60953 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9788 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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