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- PDB-5m70: Crystal Structure of human RhoGAP mutated in its arginin finger (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m70 | ||||||
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Title | Crystal Structure of human RhoGAP mutated in its arginin finger (R85A) in complex with RhoA.GDP.AlF4- human | ||||||
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![]() | SIGNALING PROTEIN / RHOGAP / Arginine finger / RHOA / transition state | ||||||
Function / homology | ![]() negative regulation of endocytic recycling / transferrin transport / 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 ...negative regulation of endocytic recycling / transferrin transport / 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 / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / negative regulation of cell size / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / RHOF GTPase cycle / negative regulation of motor neuron apoptotic process / RHOD GTPase cycle / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / regulation of small GTPase mediated signal transduction / positive regulation of alpha-beta T cell differentiation / ossification involved in bone maturation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / motor neuron apoptotic process / RND2 GTPase cycle / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / wound healing, spreading of cells / apical junction complex / regulation of neuron projection development / regulation of focal adhesion assembly / endosomal transport / negative chemotaxis / RHOB GTPase cycle / small GTPase-mediated signal transduction / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / positive regulation of cytokinesis / cerebral cortex cell migration / androgen receptor signaling pathway / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / CDC42 GTPase cycle / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / RHOG GTPase cycle / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / skeletal muscle tissue development / RHO GTPases activate PKNs / regulation of cell migration / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / GTPase activator activity / cell-matrix adhesion Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pellegrini, E. / Bowler, M.W. | ||||||
![]() | ![]() Title: Assessing the Influence of Mutation on GTPase Transition States by Using X-ray Crystallography, (19) F NMR, and DFT Approaches. Authors: Jin, Y. / Molt, R.W. / Pellegrini, E. / Cliff, M.J. / Bowler, M.W. / Richards, N.G.J. / Blackburn, G.M. / Waltho, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161 KB | Display | ![]() |
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PDB format | ![]() | 124.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 36.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5m6xC ![]() 1tx4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules AFBG
#1: Protein | Mass: 27188.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 21634.893 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Non-polymers , 4 types, 119 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: microbatch / Details: 100 mM Bis/Tris pH 5.8-6 PEG3350 23-26% |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→48.72 Å / Num. obs: 34416 / % possible obs: 98.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.502 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TX4 Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 11.511 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.258 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.384 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→20 Å
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