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Yorodumi- PDB-1i4d: CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i4d | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21) | ||||||
Components |
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Keywords | SIGNALING PROTEIN / coiled coil / G-protein / complex | ||||||
Function / homology | Function and homology information membrane curvature sensor activity / Retrograde transport at the Trans-Golgi-Network / regulation of respiratory burst / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / GTP-dependent protein binding / negative regulation of receptor-mediated endocytosis ...membrane curvature sensor activity / Retrograde transport at the Trans-Golgi-Network / regulation of respiratory burst / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / GTP-dependent protein binding / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / engulfment of apoptotic cell / NTRK2 activates RAC1 / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / respiratory burst / WNT5:FZD7-mediated leishmania damping / protein localization to phagophore assembly site / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / thioesterase binding / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / motor neuron axon guidance / PCP/CE pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / regulation of lamellipodium assembly / phosphatidylinositol-4-phosphate binding / Azathioprine ADME / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / regulation of cell size / establishment or maintenance of cell polarity / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / Rac protein signal transduction / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / mitophagy / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / Signal transduction by L1 / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / positive regulation of microtubule polymerization / ruffle / EPHB-mediated forward signaling / RAC1 GTPase cycle / regulation of cell migration / actin filament polymerization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / cell chemotaxis / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / VEGFR2 mediated vascular permeability / G protein activity / trans-Golgi network membrane / actin filament organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell motility / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / intracellular protein transport / ruffle membrane / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Tarricone, C. / Xiao, B. / Justin, N. / Gamblin, S.J. / Smerdon, S.J. | ||||||
Citation | Journal: Nature / Year: 2001 Title: The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways. Authors: Tarricone, C. / Xiao, B. / Justin, N. / Walker, P.A. / Rittinger, K. / Gamblin, S.J. / Smerdon, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i4d.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i4d.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 1i4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i4d_validation.pdf.gz | 470.5 KB | Display | wwPDB validaton report |
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Full document | 1i4d_full_validation.pdf.gz | 494.9 KB | Display | |
Data in XML | 1i4d_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1i4d_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/1i4d ftp://data.pdbj.org/pub/pdb/validation_reports/i4/1i4d | HTTPS FTP |
-Related 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: 25614.057 Da / Num. of mol.: 2 / Fragment: RESIDUES 118-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P53365 #2: Protein | | Mass: 21478.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P63000 #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-GDP / | #5: 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: 2.58 Å3/Da / Density % sol: 52.27 % | ||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Tris, Peg20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / 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: ESRF / Beamline: BM14 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 22993 / Num. obs: 21742 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.65 / Num. unique all: 2334 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / molecular replacement / Resolution: 2.5→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.3 |