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Open data
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Basic information
Entry | Database: PDB / ID: 1hh4 | ||||||
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Title | Rac1-RhoGDI complex involved in NADPH oxidase activation | ||||||
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![]() | SIGNALING PROTEIN/INHIBITOR / SINGAL PROTEIN INHIBITOR COMPLEX / SMALL G PROTEIN / GTPASE ACTIVATION / GTP-BINDING / PRENYLATION / LIPOPROTEIN / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() Rho GDP-dissociation inhibitor activity / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 ...Rho GDP-dissociation inhibitor activity / regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / regulation of synaptic vesicle cycle / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / engulfment of apoptotic cell / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / WNT5:FZD7-mediated leishmania damping / respiratory burst / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / hepatocyte growth factor receptor signaling pathway / regulation of Rho protein signal transduction / ruffle organization / thioesterase binding / regulation of stress fiber assembly / negative regulation of fibroblast migration / cell projection assembly / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / Nef and signal transduction / PCP/CE pathway / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / RHO GTPases activate KTN1 / Activation of RAC1 / motor neuron axon guidance / regulation of lamellipodium assembly / 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 / regulation of cell size / establishment or maintenance of cell polarity / DSCAM interactions / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / positive regulation of Rho protein signal transduction / NRAGE signals death through JNK / Rac protein signal transduction / RHOC GTPase cycle / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / CDC42 GTPase cycle / RHOH GTPase cycle / semaphorin-plexin signaling pathway / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / ficolin-1-rich granule membrane / immunological synapse / RHOG GTPase cycle / RHOA GTPase cycle / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / localization / RHO GTPases activate IQGAPs / anatomical structure morphogenesis / 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 / regulation of cell migration / positive regulation of microtubule polymerization / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / actin filament polymerization / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / GTPase activator activity / cell-matrix adhesion / cell chemotaxis / small monomeric GTPase / secretory granule membrane / VEGFR2 mediated vascular permeability / G protein activity / Signal transduction by L1 / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / regulation of actin cytoskeleton organization Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grizot, S. / Faure, J. / Fieschi, F. / Vignais, P.V. / Dagher, M.-C. / Pebay-Peyroula, E. | ||||||
![]() | ![]() Title: Crystal Structure of the Rac1-Rhogdi Complex Involved in Nadph Oxidase Activation Authors: Grizot, S. / Faure, J. / Fieschi, F. / Vignais, P.V. / Dagher, M.-C. / Pebay-Peyroula, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.8 KB | Display | ![]() |
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PDB format | ![]() | 116.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 35.2 KB | Display | |
Data in CIF | ![]() | 44.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1doaS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | THE ASYMMETRIC UNIT CONTAINS TWO HETERODIMERS RAC-RHOGDI,RELATED BY NCS. THE CHAIN IDENTIFIERS ARE A AND D FOR DIMER1,AND B AND E FOR DIMER 2. |
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Components
-Protein , 2 types, 4 molecules ABDE
#1: Protein | Mass: 21383.936 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 23238.096 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 36 molecules ![](data/chem/img/GDP.gif)
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | RACS ARE GTP-BINDING PROTEINS ASSOCIATED WITH PLASMA MEMBRANE WHICH COULD REGULATE SECRETORY ...RACS ARE GTP-BINDING PROTEINS ASSOCIATED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: HANGING DROP AT 20C WITH RESERVOIR: 30% PEG 4000, 100 MM NA CITRATE PH=5.6, 5 MM MGCL2, 200 MM AMMONIUM ACETATE, pH 5.60 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 21165 / % possible obs: 84.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 58.7 Å2 / Rsym value: 0.062 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.7→2.76 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.434 / % possible all: 80.6 |
Reflection | *PLUS Lowest resolution: 30 Å / Redundancy: 2.36 % / Num. measured all: 50106 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / % possible obs: 80.6 % / Redundancy: 2.28 % / Rmerge(I) obs: 0.434 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DOA Resolution: 2.7→19.8 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0 Details: TWO GROUPS WERE DEFINED FOR NCS RESTRAINTS, GROUP 1 BETWEEN CHAIN ID A AND B (ALL RESIDUES EXCEPT 28 - 40 AND 178 - 189), GROUP2 BETWEEN CHAIN ID D AND E (RESIDUES 330 - 353 AND 390 - 500)
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.5 Å2 / ksol: 0.29 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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