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Yorodumi- PDB-4f38: Crystal structure of geranylgeranylated RhoA in complex with RhoG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f38 | ||||||
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Title | Crystal structure of geranylgeranylated RhoA in complex with RhoGDI in its active GPPNHP-bound form | ||||||
Components |
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Keywords | CELL CYCLE/CHAPERONE / RhoA / RhoGDI / active GPPNHP bound form / CELL CYCLE-CHAPERONE complex | ||||||
Function / homology | Function and homology information RHO GTPases Activate ROCKs / SLIT2:ROBO1 increases RHOA activity / cellular response to redox state / Sema4D mediated inhibition of cell attachment and migration / Sema4D induced cell migration and growth-cone collapse / : / RHO GTPases Activate Rhotekin and Rhophilins / RHO GTPases activate PKNs / Axonal growth stimulation / PCP/CE pathway ...RHO GTPases Activate ROCKs / SLIT2:ROBO1 increases RHOA activity / cellular response to redox state / Sema4D mediated inhibition of cell attachment and migration / Sema4D induced cell migration and growth-cone collapse / : / RHO GTPases Activate Rhotekin and Rhophilins / RHO GTPases activate PKNs / Axonal growth stimulation / PCP/CE pathway / RHO GTPases activate KTN1 / : / small GTPase binding => GO:0031267 / small GTPase binding => GO:0031267 / Axonal growth inhibition (RHOA activation) / PI3K/AKT activation / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / EPHA-mediated growth cone collapse / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / Rho GDP-dissociation inhibitor activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / G beta:gamma signalling through PI3Kgamma / negative regulation of synapse assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RHOA GTPase cycle / RHO GTPases activate CIT / Ovarian tumor domain proteases / G alpha (12/13) signalling events / regulation of dendrite development / RHO GTPases Activate Formins / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / regulation of modification of synaptic structure / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / negative regulation of vascular associated smooth muscle cell migration / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / positive regulation of smooth muscle contraction / regulation of osteoblast proliferation / 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 / negative regulation of cell size / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / VEGFA-VEGFR2 Pathway / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / apolipoprotein A-I-mediated signaling pathway / GTP metabolic process / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / stress-activated protein kinase signaling cascade / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / odontogenesis / motor neuron apoptotic process / microtubule depolymerization / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of neuron projection development / negative chemotaxis / apical junction complex / Rho GDP-dissociation inhibitor binding / myosin binding / positive regulation of actin filament polymerization / stress fiber assembly / positive regulation of cytokinesis / androgen receptor signaling pathway / cerebral cortex cell migration / cellular response to cytokine stimulus / negative regulation of vascular associated smooth muscle cell proliferation / cleavage furrow / regulation of calcium ion transport / semaphorin-plexin signaling pathway / Rho protein signal transduction / immunological synapse / negative regulation of neuron differentiation / mitotic spindle assembly / cellular response to organic cyclic compound / endothelial cell migration / positive regulation of T cell migration / regulation of microtubule cytoskeleton organization / negative regulation of canonical NF-kappaB signal transduction / cytoplasmic microtubule organization Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Guo, Z. / Tnimov, Z. / Alexandrov, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Quantitative Analysis of Prenylated RhoA Interaction with Its Chaperone, RhoGDI. Authors: Tnimov, Z. / Guo, Z. / Gambin, Y. / Nguyen, U.T. / Wu, Y.W. / Abankwa, D. / Stigter, A. / Collins, B.M. / Waldmann, H. / Goody, R.S. / Alexandrov, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f38.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f38.ent.gz | 131.8 KB | Display | PDB format |
PDBx/mmJSON format | 4f38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/4f38 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/4f38 | HTTPS FTP |
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-Related structure data
Related structure data | 1doaS S: Starting model for refinement |
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Similar 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: 21994.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rhoa, Arha, Arha2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9QUI0*PLUS |
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#2: Protein | Mass: 23379.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arhgdia, C87222, Gdi1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q99PT1*PLUS |
-Non-polymers , 4 types, 84 molecules
#3: Chemical | ChemComp-GER / | ||||
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#4: Chemical | #5: Chemical | ChemComp-GNP / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | SEQUENCE REFERENCES |
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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: 2.47 Å3/Da / Density % sol: 50.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 20% (w/v) PEG 3350, 0.2M MgCl2, 0.1M Hepes-NaOH, 25mM Hepes-NaOH pH 7.2, 40mM NaCl, 3mM MgCl2, 10M GMPPNP, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→68.01 Å / Num. all: 21383 / Num. obs: 20741 / % possible obs: 97 % / Observed criterion σ(F): 6.9 / Observed criterion σ(I): 12.33 / Redundancy: 2.7 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.07 / Net I/σ(I): 12.33 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2156 / Rsym value: 0.279 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DOA Resolution: 2.8→68.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.867 / SU B: 34.184 / SU ML: 0.316 / Cross valid method: THROUGHOUT / σ(F): 3.6 / σ(I): 3.6 / ESU R Free: 0.429 / 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: 37.387 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→68.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 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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