+Open data
-Basic information
Entry | Database: PDB / ID: 5cjp | ||||||
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Title | The Structural Basis for Cdc42-Induced Dimerization of IQGAPs | ||||||
Components |
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Keywords | PROTEIN BINDING / IQGAP2 GAP related domain X-ray GTPase interactions Complex Cdc42 | ||||||
Function / homology | Function and homology information : / mitotic actomyosin contractile ring assembly actin filament organization / : / establishment or maintenance of apical/basal cell polarity / protein localization => GO:0008104 / thrombin-activated receptor signaling pathway / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex ...: / mitotic actomyosin contractile ring assembly actin filament organization / : / establishment or maintenance of apical/basal cell polarity / protein localization => GO:0008104 / thrombin-activated receptor signaling pathway / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / Arp2/3 complex-mediated actin nucleation / positive regulation of pinocytosis / Arp2/3 complex binding / 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 / storage vacuole / GTPase inhibitor activity / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / regulation of protein binding / 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 / cardiac conduction system development / Inactivation of CDC42 and RAC1 / establishment of Golgi localization / leading edge membrane / regulation of filopodium assembly / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / mitogen-activated protein kinase kinase kinase binding / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / nuclear migration / regulation of lamellipodium assembly / adherens junction organization / sprouting angiogenesis / DCC mediated attractive signaling / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / positive regulation of filopodium assembly / regulation of postsynapse organization / regulation of mitotic nuclear division / RHOV GTPase cycle / establishment or maintenance of cell polarity / phagocytosis, engulfment / heart contraction / positive regulation of DNA replication / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / phosphatidylinositol-3,4,5-trisphosphate binding / microvillus / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / 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 / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / EGFR downregulation / small monomeric GTPase / secretory granule membrane / G protein activity / secretory granule / filopodium / actin filament organization / cell projection / integrin-mediated signaling pathway / RHO GTPases Activate Formins Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Worthylake, D.K. / Boyapati, V.K. / LeCour Jr, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2016 Title: The Structural Basis for Cdc42-Induced Dimerization of IQGAPs. Authors: LeCour, L. / Boyapati, V.K. / Liu, J. / Li, Z. / Sacks, D.B. / Worthylake, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cjp.cif.gz | 302.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cjp.ent.gz | 242.6 KB | Display | PDB format |
PDBx/mmJSON format | 5cjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cjp_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5cjp_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5cjp_validation.xml.gz | 59.8 KB | Display | |
Data in CIF | 5cjp_validation.cif.gz | 79.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/5cjp ftp://data.pdbj.org/pub/pdb/validation_reports/cj/5cjp | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19758.748 Da / Num. of mol.: 4 / Mutation: Q61L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42, hCG_1981007 / Plasmid: pPRO EX HTb Details (production host): plasmid encodes a TEV protease cleavable 6xHis tag which leaves a Gly-Ala cloning artifact preceding the initiator methionine Cell line (production host): RIL / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: A0A024RAE4, UniProt: P60953*PLUS #2: Protein | Mass: 44058.094 Da / Num. of mol.: 2 / Fragment: unp reesidues 875-1258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IQGAP2 / Plasmid: pET Trx Details (production host): kanamycin, encodes E. coli thioredoxin and a TEV protease-cleavable 6xHis tag N-terminal to the IQGAP2 GAP-related domain Cell line (production host): RIL / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q13576 #3: Chemical | ChemComp-GTP / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.01 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 28.5% (v/v) polyethylene glycol (PEG) MW 400, 100mM 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.5 and 40mM MgCl2. PH range: 6.5-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 12, 2014 |
Radiation | Monochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→20 Å / Num. obs: 61742 / % possible obs: 99.7 % / Redundancy: 7.3 % / Net I/av σ(I): 2.9 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.57→2.71 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 2.6→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Solvent computation | Bsol: 33.9884 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 198.96 Å2 / Biso mean: 72.6528 Å2 / Biso min: 19.35 Å2
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Refinement step | Cycle: final / Resolution: 2.6→20 Å
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Refine LS restraints | Type: c_angle_d / Dev ideal: 1.314 |