+Open data
-Basic information
Entry | Database: PDB / ID: 1hh4 | ||||||
---|---|---|---|---|---|---|---|
Title | Rac1-RhoGDI complex involved in NADPH oxidase activation | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN/INHIBITOR / SINGAL PROTEIN INHIBITOR COMPLEX / SMALL G PROTEIN / GTPASE ACTIVATION / GTP-BINDING / PRENYLATION / LIPOPROTEIN / SIGNALING PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly ...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 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / regulation of synaptic vesicle cycle / WNT5:FZD7-mediated leishmania damping / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / regulation of Rho protein signal transduction / 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 / sphingosine-1-phosphate receptor signaling pathway / 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 / lamellipodium assembly / 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 / Rho GDP-dissociation inhibitor binding / NRAGE signals death through JNK / Rac protein signal transduction / RHOC GTPase cycle / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / RHOH GTPase cycle / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / Rho protein signal transduction / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / immunological synapse / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / GTPase activator activity / cell chemotaxis / substrate adhesion-dependent cell spreading / cell-matrix adhesion / small monomeric GTPase / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / cell projection / actin filament organization / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Grizot, S. / Faure, J. / Fieschi, F. / Vignais, P.V. / Dagher, M.-C. / Pebay-Peyroula, E. | ||||||
Citation | Journal: Biochemistry / Year: 2001 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1hh4.cif.gz | 147.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1hh4.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/1hh4 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/1hh4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1doaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
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. |
-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.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P15154, UniProt: P63000*PLUS #2: Protein | Mass: 23238.096 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P52565 |
---|
-Non-polymers , 4 types, 36 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Compound details | RACS ARE GTP-BINDING PROTEINS ASSOCIATED WITH PLASMA MEMBRANE WHICH COULD REGULATE SECRETORY ...RACS ARE GTP-BINDING PROTEINS ASSOCIATED |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.95 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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)
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.5 Å2 / ksol: 0.29 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
|