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Yorodumi- PDB-1ki1: Guanine Nucleotide Exchange Region of Intersectin in Complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ki1 | ||||||
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Title | Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42 | ||||||
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Keywords | SIGNALING PROTEIN / Protein-Protein complex / DH domain / PH domain / Rho GTPase | ||||||
Function / homology | Function and homology information clathrin-dependent synaptic vesicle endocytosis / 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 ...clathrin-dependent synaptic vesicle endocytosis / 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 / intracellular vesicle / 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 / establishment of Golgi localization / leading edge membrane / regulation of filopodium assembly / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / mitogen-activated protein kinase kinase kinase binding / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / proline-rich region binding / nuclear migration / regulation of lamellipodium assembly / adherens junction organization / sprouting angiogenesis / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / positive regulation of filopodium assembly / regulation of postsynapse organization / endosomal transport / regulation of mitotic nuclear division / RHOV GTPase cycle / establishment or maintenance of cell polarity / phagocytosis, engulfment / heart contraction / positive regulation of DNA replication / NRAGE signals death through JNK / Myogenesis / RHOJ GTPase cycle / Golgi organization / exocytosis / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / 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 / clathrin-coated pit / phagocytic vesicle / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / EGFR downregulation / small monomeric GTPase / G protein activity / guanyl-nucleotide exchange factor activity / secretory granule / filopodium / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / FCGR3A-mediated phagocytosis / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / recycling endosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Snyder, J.T. / Pruitt, W.M. / Der, C.J. / Sondek, J. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Structural basis for the selective activation of Rho GTPases by Dbl exchange factors. Authors: Snyder, J.T. / Worthylake, D.K. / Rossman, K.L. / Betts, L. / Pruitt, W.M. / Siderovski, D.P. / Der, C.J. / Sondek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ki1.cif.gz | 218.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ki1.ent.gz | 176.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ki1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ki1_validation.pdf.gz | 403.7 KB | Display | wwPDB validaton report |
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Full document | 1ki1_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 1ki1_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 1ki1_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/1ki1 ftp://data.pdbj.org/pub/pdb/validation_reports/ki/1ki1 | HTTPS FTP |
-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: 20942.070 Da / Num. of mol.: 2 / Fragment: residues 1-188 / Mutation: C188S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P60953 #2: Protein | Mass: 40936.523 Da / Num. of mol.: 2 Fragment: Dbl homology and Pleckstrin homology domains (residues 1229-1580) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15811 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.42 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 4000, ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X4A / Wavelength: 0.9787, 0.9792 | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 2000 | |||||||||
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→30 Å / Num. all: 64188 / Num. obs: 61357 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 / Rsym value: 0.083 / Net I/σ(I): 34 | |||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.2 / Num. unique all: 5135 / Rsym value: 0.256 / % possible all: 80.5 | |||||||||
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 55366 / % possible obs: 85.3 % / Num. measured all: 572588 / Rmerge(I) obs: 0.076 | |||||||||
Reflection shell | *PLUS % possible obs: 79.6 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 7 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2.3→15 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å /
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.231 / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.231 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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