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Open data
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Basic information
Entry | Database: PDB / ID: 1grn | ||||||
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Title | CRYSTAL STRUCTURE OF THE CDC42/CDC42GAP/ALF3 COMPLEX. | ||||||
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![]() | GENE REGULATION / TRANSITION-STATE / G-PROTEIN / CDC42 / GAP / ALF3 | ||||||
Function / homology | ![]() negative regulation of endocytic recycling / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis ...negative regulation of endocytic recycling / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / neuron fate determination / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / host-mediated perturbation of viral process / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / GTP-dependent protein binding / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / RHOD GTPase cycle / embryonic heart tube development / RHOF GTPase cycle / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / positive regulation of filopodium assembly / Wnt signaling pathway, planar cell polarity pathway / RND2 GTPase cycle / endosomal transport / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOB GTPase cycle / RHOV GTPase cycle / nuclear migration / small GTPase-mediated signal transduction / Myogenesis / heart contraction / positive regulation of cytokinesis / establishment of cell polarity / spindle midzone / establishment or maintenance of cell polarity / RHOC GTPase cycle / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / Rho protein signal transduction / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / ruffle / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of substrate adhesion-dependent cell spreading / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / actin filament organization / EGFR downregulation / transferrin transport / small monomeric GTPase / integrin-mediated signaling pathway / MAPK6/MAPK4 signaling / FCGR3A-mediated phagocytosis / regulation of actin cytoskeleton organization / filopodium / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / SH3 domain binding / cellular response to type II interferon / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis / G beta:gamma signalling through CDC42 / apical part of cell Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nassar, N. / Hoffman, G.R. / Clardy, J.C. / Cerione, R.A. | ||||||
![]() | ![]() Title: Structures of Cdc42 bound to the active and catalytically compromised forms of Cdc42GAP. Authors: Nassar, N. / Hoffman, G.R. / Manor, D. / Clardy, J.C. / Cerione, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.3 KB | Display | ![]() |
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PDB format | ![]() | 69.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.8 KB | Display | ![]() |
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Full document | ![]() | 474.3 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 21283.582 Da / Num. of mol.: 1 / Fragment: CDC42 Source method: isolated from a genetically manipulated source Details: GDP, MG++, ALF3 / Source: (gene. exp.) ![]() Description: PROTEINS EXPRESSED IN ESCHERICHIA COLI AS HIS-TAGGED FUSION PROTEINS.; Cellular location: CYTOPLASM / Production host: ![]() ![]() |
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#2: Protein | Mass: 23044.260 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN OF CDC42GAP Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: PROTEINS EXPRESSED IN ESCHERICHIA COLI AS HIS-TAGGED FUSION PROTEINS. Cellular location: CYTOPLASM / Production host: ![]() ![]() |
-Non-polymers , 4 types, 75 molecules 






#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-GDP / |
#5: Chemical | ChemComp-AF3 / |
#6: Water | ChemComp-HOH / |
-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 49 % Description: THE STRUCTURE WAS SOLVED BY A COMBINATION OF MAD PHASING AND MOLECULAR REPLACEMENT. | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 23543 / % possible obs: 85.9 % / Redundancy: 5.6 % / Rsym value: 0.064 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2.1→2.2 Å / Mean I/σ(I) obs: 9.3 / Rsym value: 0.331 / % possible all: 85.9 |
Reflection | *PLUS Num. measured all: 129060 / Rmerge(I) obs: 0.064 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: CDC42 IN THE GTP FORM Resolution: 2.1→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THE AL AND F ATOMS WERE RESTRAINED TO BE PLANAR.
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % reflection Rfree: 10 % |