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Yorodumi- PDB-5c2k: Crystal structure of the fusion protein linked by RhoA and the GA... -
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-Basic information
Entry | Database: PDB / ID: 5c2k | ||||||
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Title | Crystal structure of the fusion protein linked by RhoA and the GAP domain of MgcRacGAP | ||||||
Components | Transforming protein RhoA,Rac GTPase-activating protein 1 | ||||||
Keywords | HYDROLASE ACTIVATOR / GTPase activation / fusion protein / small G protein | ||||||
Function / homology | Function and homology information centralspindlin complex / actomyosin contractile ring assembly / sulfate transport / mitotic spindle midzone assembly / aortic valve formation / alpha-beta T cell lineage commitment / regulation of attachment of spindle microtubules to kinetochore / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity ...centralspindlin complex / actomyosin contractile ring assembly / sulfate transport / mitotic spindle midzone assembly / aortic valve formation / alpha-beta T cell lineage commitment / regulation of attachment of spindle microtubules to kinetochore / 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 / 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 / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / gamma-tubulin binding / RHOD GTPase cycle / RHO GTPases activate CIT / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / Kinesins / Flemming body / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / regulation of small GTPase mediated signal transduction / 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 / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / wound healing, spreading of cells / COPI-dependent Golgi-to-ER retrograde traffic / regulation of neuron projection development / regulation of focal adhesion assembly / apical junction complex / negative chemotaxis / RHOB GTPase cycle / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / beta-tubulin binding / RHOC GTPase cycle / positive regulation of cytokinesis / androgen receptor signaling pathway / cerebral cortex cell migration / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / regulation of embryonic development / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic cytokinesis / alpha-tubulin binding / mitotic spindle assembly / neuroblast proliferation / RHOA GTPase cycle / endothelial cell migration / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of T cell migration / spindle midzone / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / monoatomic ion transport / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / RHO GTPases activate PKNs / skeletal muscle tissue development / regulation of cell migration / positive regulation of stress fiber assembly Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Murayama, K. / Kato-Murayama, M. / Hosaka, T. / Kitamura, T. / Yokoyama, S. / Shirouzu, M. | ||||||
Citation | Journal: To Be Published Title: Structural basis of G-protein target alternation of MgcRacGAP by phospholylation Authors: Murayama, K. / Kato-Murayama, M. / Hosaka, T. / kawashima, T. / Kitamura, T. / Yokoyama, S. / Shirouzu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c2k.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c2k.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 5c2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/5c2k ftp://data.pdbj.org/pub/pdb/validation_reports/c2/5c2k | HTTPS FTP |
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-Related structure data
Related structure data | 5c2jC 1tx4S 2ovjS C: citing same article (ref.) 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
#1: Protein | Mass: 46070.906 Da / Num. of mol.: 1 / Fragment: GAP domain, UNP residues 346-546 / Mutation: S249D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, RACGAP1 / Plasmid: pCR2.1 / Production host: Cell-free synthesis (others) / References: UniProt: P61586, UniProt: Q9H0H5 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-AF3 / |
#4: Chemical | ChemComp-GDP / |
#5: Water | ChemComp-HOH / |
Sequence details | This sequence is based on GenBank BAA90247. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG3350, Bis-Tris |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→50 Å / Num. obs: 73586 / % possible obs: 99.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 16.5 Å2 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.42→1.47 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.47 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OVJ , 1TX4 Resolution: 1.42→32.26 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 975869.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.9972 Å2 / ksol: 0.378865 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: 1 / Resolution: 1.42→32.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.51 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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