+Open data
-Basic information
Entry | Database: PDB / ID: 2rgn | ||||||
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Title | Crystal Structure of p63RhoGEF complex with Galpha-q and RhoA | ||||||
Components |
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Keywords | SIGNALING PROTEIN complex / Heterotrimeric G-protein / small molecular weight G-protein / signaling complex / protein-protein complex / RhoGEF / RhoA / GalphaQ / Galpha-Q / p63RhoGEF / Gq / GTP-binding / Lipoprotein / Nucleotide-binding / Palmitate / Transducer / ADP-ribosylation / Cytoskeleton / Magnesium / Membrane / Methylation / Prenylation / Proto-oncogene | ||||||
Function / homology | Function and homology information guanyl-nucleotide exchange factor activity => GO:0005085 / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / Extra-nuclear estrogen signaling ...guanyl-nucleotide exchange factor activity => GO:0005085 / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / Extra-nuclear estrogen signaling / G-protein activation / Adenylate cyclase inhibitory pathway / G alpha (q) signalling events / endothelin receptor signaling pathway / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / developmental pigmentation / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / phospholipase C-activating dopamine receptor signaling pathway / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / cranial skeletal system development / negative regulation of intracellular steroid hormone receptor signaling pathway / regulation of platelet activation / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / ADP signalling through P2Y purinoceptor 1 / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / maternal behavior / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / regulation of Rho protein signal transduction / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / negative regulation of cell size / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / glutamate receptor signaling pathway / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / G alpha (i) signalling events / apolipoprotein A-I-mediated signaling pathway / regulation of canonical Wnt signaling pathway / negative regulation of synaptic transmission / positive regulation of podosome assembly / alkylglycerophosphoethanolamine phosphodiesterase activity / negative regulation of cell-substrate adhesion / GTPase activating protein binding / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / odontogenesis / motor neuron apoptotic process / wound healing, spreading of cells / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / action potential / regulation of focal adhesion assembly / neuron remodeling / negative chemotaxis / myosin binding / embryonic digit morphogenesis / myofibril / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / ligand-gated ion channel signaling pathway / cleavage furrow / negative regulation of potassium ion transport / semaphorin-plexin signaling pathway Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å | ||||||
Authors | Shankaranarayanan, A. / Nance, M.R. / Tesmer, J.J.G. | ||||||
Citation | Journal: Science / Year: 2007 Title: Structure of Galphaq-p63RhoGEF-RhoA complex reveals a pathway for the activation of RhoA by GPCRs. Authors: Lutz, S. / Shankaranarayanan, A. / Coco, C. / Ridilla, M. / Nance, M.R. / Vettel, C. / Baltus, D. / Evelyn, C.R. / Neubig, R.R. / Wieland, T. / Tesmer, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rgn.cif.gz | 344.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rgn.ent.gz | 269.7 KB | Display | PDB format |
PDBx/mmJSON format | 2rgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/2rgn ftp://data.pdbj.org/pub/pdb/validation_reports/rg/2rgn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 2
NCS ensembles :
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Details | Biological unit is a trimer. Chains A, B, and C form one biological unit. Chains D, E, and F form a second biological unit. |
-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 41298.895 Da / Num. of mol.: 2 Fragment: Chimeric protein of rat Guanine nucleotide-binding protein G(i) subunit alpha-1 N-terminal helix residues 1-28 and mouse Guanine nucleotide-binding protein G(q) subunit alpha residues 31- ...Fragment: Chimeric protein of rat Guanine nucleotide-binding protein G(i) subunit alpha-1 N-terminal helix residues 1-28 and mouse Guanine nucleotide-binding protein G(q) subunit alpha residues 31-353,Chimeric protein of rat Guanine nucleotide-binding protein G(i) subunit alpha-1 N-terminal helix residues 1-28 and mouse Guanine nucleotide-binding protein G(q) subunit alpha residues 31-353 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse) Genus: Mus / Gene: Gnai1, Gnai-1, Gnaq / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High 5 / References: UniProt: P10824, UniProt: P21279*PLUS #2: Protein | Mass: 40605.383 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF25, GEFT / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE-3 pLysS / References: UniProt: Q86VW2 #3: Protein | Mass: 22132.498 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pMal c2t H10 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta De-3 pLysS / References: UniProt: P61586 |
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-Non-polymers , 4 types, 12 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.98 Å3/Da / Density % sol: 58.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM HEPES pH 6.5, 14.5% PEG 3350, 400 mM KCl. Drops were microseeded to obtain large crystals, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9993 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9993 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→30 Å / Num. all: 30174 / Num. obs: 29299 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Χ2: 1.038 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 3.5→3.62 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.67 / Num. unique all: 2976 / Rsym value: 0.53 / Χ2: 0.929 / % possible all: 98.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2bcj (Galpha-Q), 1lb1 (RhoA; Dbs for p63) Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.932 / SU B: 60.302 / SU ML: 0.429 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 124.405 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.5→3.588 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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