+Open data
-Basic information
Entry | Database: PDB / ID: 1tx4 | ||||||
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Title | RHO/RHOGAP/GDP(DOT)ALF4 COMPLEX | ||||||
Components |
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Keywords | COMPLEX(GTPASE ACTIVATN/PROTO-ONCOGENE) / COMPLEX (GTPASE ACTIVATION-PROTO-ONCOGENE) / GTPASE / TRANSITION STATE / GAP / COMPLEX(GTPASE ACTIVATN-PROTO-ONCOGENE) COMPLEX | ||||||
Function / homology | Function and homology information 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 / 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 / RHOF GTPase cycle / RHO GTPases activate CIT / RHOD GTPase cycle / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / positive regulation of alpha-beta T cell differentiation / ossification involved in bone maturation / odontogenesis / motor neuron apoptotic process / wound healing, spreading of cells / RND2 GTPase cycle / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / endosomal transport / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / RHOB GTPase cycle / small GTPase-mediated signal transduction / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOJ GTPase cycle / RHOC GTPase cycle / RHOQ GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOG GTPase cycle / RHOA GTPase cycle / endothelial cell migration / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cytoplasmic microtubule organization / regulation of microtubule cytoskeleton organization / skeletal muscle tissue development / negative regulation of reactive oxygen species biosynthetic process / regulation of cell migration / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / GTPase activator activity / cell-matrix adhesion / substrate adhesion-dependent cell spreading Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Rittinger, K. / Walker, P.A. / Smerdon, S.J. / Gamblin, S.J. | ||||||
Citation | Journal: Nature / Year: 1997 Title: Structure at 1.65 A of RhoA and its GTPase-activating protein in complex with a transition-state analogue. Authors: Rittinger, K. / Walker, P.A. / Eccleston, J.F. / Smerdon, S.J. / Gamblin, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tx4.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tx4.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/1tx4 ftp://data.pdbj.org/pub/pdb/validation_reports/tx/1tx4 | HTTPS FTP |
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-Related structure data
Related structure data | 1am4S 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: 22586.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q07960 |
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#2: Protein | Mass: 20032.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P61586 |
-Non-polymers , 4 types, 500 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-ALF / |
#5: Chemical | ChemComp-GDP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: PROTEIN WAS CRYSTALLIZED FROM 18% PEG 2000 MME 100MM MES PH6.0 10MM MGCL2, 3MM DTT, 3MM NAN3, 114MM AMMONIUM SULFATE 400UM PROTEIN COMPLEX WITH 1MM ALCL3 AND 10MM NAF. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLAGE / Date: Jun 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→6 Å / Num. obs: 42992 / % possible obs: 80.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.65→1.72 Å / % possible all: 60.8 |
Reflection | *PLUS Num. measured all: 160124 |
Reflection shell | *PLUS % possible obs: 60.8 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AM4 Resolution: 1.65→6 Å
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Refinement step | Cycle: LAST / Resolution: 1.65→6 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.169 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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