+Open data
-Basic information
Entry | Database: PDB / ID: 1grn | ||||||
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Title | CRYSTAL STRUCTURE OF THE CDC42/CDC42GAP/ALF3 COMPLEX. | ||||||
Components |
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Keywords | GENE REGULATION / TRANSITION-STATE / G-PROTEIN / CDC42 / GAP / ALF3 | ||||||
Function / homology | Function and homology information negative regulation of endocytic recycling / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis ...negative regulation of endocytic recycling / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / transferrin transport / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / modulation by host of viral process / GTP-dependent protein binding / 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 / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / mitogen-activated protein kinase kinase kinase binding / dendritic spine morphogenesis / thioesterase binding / RHOF GTPase cycle / embryonic heart tube development / regulation of stress fiber assembly / RHOD GTPase cycle / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / regulation of small GTPase mediated signal transduction / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / RND2 GTPase cycle / positive regulation of filopodium assembly / regulation of postsynapse organization / endosomal transport / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / RHOB GTPase cycle / heart contraction / Myogenesis / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / Golgi organization / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / Rho protein signal transduction / macrophage differentiation / RHOG GTPase cycle / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / RAC3 GTPase cycle / spindle midzone / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / phagocytic vesicle / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / small monomeric GTPase / G protein activity / secretory granule / positive regulation of DNA replication / filopodium / integrin-mediated signaling pathway / RHO GTPases Activate Formins / actin filament organization / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / EGFR downregulation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Nassar, N. / Hoffman, G.R. / Clardy, J.C. / Cerione, R.A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1998 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1grn.cif.gz | 93 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1grn.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 1grn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gr/1grn ftp://data.pdbj.org/pub/pdb/validation_reports/gr/1grn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) Description: PROTEINS EXPRESSED IN ESCHERICHIA COLI AS HIS-TAGGED FUSION PROTEINS.; Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P60953 |
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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.) Homo sapiens (human) Description: PROTEINS EXPRESSED IN ESCHERICHIA COLI AS HIS-TAGGED FUSION PROTEINS. Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q07960 |
-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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.92 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD 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: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 % |