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Yorodumi- PDB-1kz7: Crystal Structure of the DH/PH Fragment of Murine Dbs in Complex ... -
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-Basic information
Entry | Database: PDB / ID: 1kz7 | ||||||
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Title | Crystal Structure of the DH/PH Fragment of Murine Dbs in Complex with the Placental Isoform of Human Cdc42 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / guanine nucleotide exchange factor (GEF) / small G-protein | ||||||
Function / homology | Function and homology information RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / 1-phosphatidylinositol binding / NRAGE signals death through JNK / GBD domain binding / submandibular salivary gland formation / actin filament branching / RAC1 GTPase cycle ...RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / 1-phosphatidylinositol binding / NRAGE signals death through JNK / GBD domain binding / submandibular salivary gland formation / actin filament branching / RAC1 GTPase cycle / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / RHOG GTPase cycle / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / G alpha (12/13) signalling events / 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 / GTP-dependent protein binding / 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 / 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 / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / positive regulation of Rho protein signal transduction / regulation of mitotic nuclear division / establishment or maintenance of cell polarity / phagocytosis, engulfment / RHOV GTPase cycle / extrinsic component of membrane / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / Rho protein signal transduction / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / endomembrane system / 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 / extrinsic component of cytoplasmic side of plasma membrane / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / phosphatidylinositol binding / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / filopodium / positive regulation of DNA replication / secretory granule / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Rossman, K.L. / Worthylake, D.K. / Snyder, J.T. / Siderovski, D.P. / Campbell, S.L. / Sondek, J. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: A crystallographic view of interactions between Dbs and Cdc42: PH domain-assisted guanine nucleotide exchange. Authors: Rossman, K.L. / Worthylake, D.K. / Snyder, J.T. / Siderovski, D.P. / Campbell, S.L. / Sondek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kz7.cif.gz | 220.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kz7.ent.gz | 181.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kz7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/1kz7 ftp://data.pdbj.org/pub/pdb/validation_reports/kz/1kz7 | HTTPS FTP |
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-Related 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: 41710.141 Da / Num. of mol.: 2 / Fragment: DH/PH fragment (residues 623-967) / Mutation: E940A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dbs / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q64096 #2: Protein | Mass: 20942.070 Da / Num. of mol.: 2 / Fragment: residues 1-188 / Mutation: C188S Source method: isolated from a genetically manipulated source Details: PLACENTAL ISOFORM / Source: (gene. exp.) Homo sapiens (human) / Gene: Cdc42 / Plasmid: pET-21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60953 #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: 2.69 Å3/Da / Density % sol: 54.27 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 8000, sodium formate, Tris HCL, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2000 |
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 46595 / Num. obs: 46595 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 31.1 Å2 / Limit h max: 26 / Limit h min: 0 / Limit k max: 31 / Limit k min: 0 / Limit l max: 91 / Limit l min: 0 / Observed criterion F max: 1908848.01 / Observed criterion F min: 5.5 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 58 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Num. obs: 49528 / Num. measured all: 418244 / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS % possible obs: 58 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→19.99 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 36.4139 Å2 / ksol: 0.359574 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.35 Å2 / Biso mean: 41.82 Å2 / Biso min: 12.95 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.99 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: 8
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Rfactor obs: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.236 |