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Yorodumi- PDB-1foe: CRYSTAL STRUCTURE OF RAC1 IN COMPLEX WITH THE GUANINE NUCLEOTIDE ... -
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-Basic information
Entry | Database: PDB / ID: 1foe | ||||||
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Title | CRYSTAL STRUCTURE OF RAC1 IN COMPLEX WITH THE GUANINE NUCLEOTIDE EXCHANGE REGION OF TIAM1 | ||||||
Components |
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Keywords | signaling protein / immune system/signaling protein / DBL HOMOLOGY DOMAIN / PLECKSTRIN HOMOLOGY DOMAIN / GTPASE / GUANINE NUCLEOTIDE EXCHANGE FACTOR / immune system-signaling protein COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of Schwann cell chemotaxis / brain-derived neurotrophic factor receptor signaling pathway / RAC3 GTPase cycle / regulation of non-canonical Wnt signaling pathway / RAC2 GTPase cycle / regulation of dopaminergic neuron differentiation / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / EPHB-mediated forward signaling ...positive regulation of Schwann cell chemotaxis / brain-derived neurotrophic factor receptor signaling pathway / RAC3 GTPase cycle / regulation of non-canonical Wnt signaling pathway / RAC2 GTPase cycle / regulation of dopaminergic neuron differentiation / CDC42 GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / EPHB-mediated forward signaling / NRAGE signals death through JNK / extrinsic component of postsynaptic density membrane / RAC1 GTPase cycle / kinocilium / regulation of respiratory burst / negative regulation of interleukin-23 production / G alpha (12/13) signalling events / regulation of neutrophil migration / localization within membrane / NMDA selective glutamate receptor signaling pathway / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / regulation of epithelial to mesenchymal transition / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / positive regulation of dendritic spine morphogenesis / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of modification of postsynaptic actin cytoskeleton / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / cell-cell contact zone / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / protein localization to membrane / cardiac muscle hypertrophy / sphingosine-1-phosphate receptor signaling pathway / activation of GTPase activity / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / regulation of postsynapse organization / lamellipodium assembly / main axon / neuron projection extension / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / positive regulation of axonogenesis / Rho GDP-dissociation inhibitor binding / regulation of GTPase activity / NRAGE signals death through JNK / Rac protein signal transduction / pericentriolar material / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RHO GTPases activate IQGAPs / ephrin receptor signaling pathway / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / axonal growth cone / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / somatodendritic compartment Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Worthylake, D.K. / Rossman, K.L. / Sondek, J. | ||||||
Citation | Journal: Nature / Year: 2000 Title: Crystal structure of Rac1 in complex with the guanine nucleotide exchange region of Tiam1. Authors: Worthylake, D.K. / Rossman, K.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 | 1foe.cif.gz | 435.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1foe.ent.gz | 366.6 KB | Display | PDB format |
PDBx/mmJSON format | 1foe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/1foe ftp://data.pdbj.org/pub/pdb/validation_reports/fo/1foe | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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7 |
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Unit cell |
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Details | The biological assembly is a heterodimer composed of a Tiam1 Dbl/pleckstrin element (chains A,C,E,G) in complex with a Rac1 molecule (Chains B,D,F,H). There are 4 heterodimers in the crystal asymmetric unit |
-Components
#1: Protein | Mass: 43827.539 Da / Num. of mol.: 4 Fragment: RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN Mutation: ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS Source method: isolated from a genetically manipulated source Details: ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PPROEXHTA / Production host: Escherichia coli (E. coli) / References: UniProt: Q60610 #2: Protein | Mass: 19710.764 Da / Num. of mol.: 4 / Fragment: RESIDUES 1 TO 177 FROM HUMAN RAC1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / References: UniProt: P63000 #3: Chemical | ChemComp-SO4 / #4: 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: 3.51 Å3/Da / Density % sol: 64.95 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6 Details: PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting 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: 0.9729,0.9787,0.9724 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 16, 1999 | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→15 Å / Num. all: 80441 / Num. obs: 80441 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 27.9 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.392 / Num. unique all: 5874 / % possible all: 68.9 | ||||||||||||
Reflection | *PLUS % possible obs: 94.2 % / Num. measured all: 382085 | ||||||||||||
Reflection shell | *PLUS % possible obs: 68.9 % / Mean I/σ(I) obs: 4.3 |
-Processing
Software |
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Refinement | Resolution: 2.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: Used maximum likelihood target function in CNS
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.262 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.4 |