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Yorodumi- PDB-1kmq: Crystal Structure of a Constitutively Activated RhoA Mutant (Q63L) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kmq | ||||||
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Title | Crystal Structure of a Constitutively Activated RhoA Mutant (Q63L) | ||||||
Components | TRANSFORMING PROTEIN RHOA | ||||||
Keywords | SIGNALING PROTEIN / GTPase / constitutive mutant / GTP-analog | ||||||
Function / homology | Function and homology information 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 ...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 / cerebral cortex cell migration / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / beta selection / establishment of epithelial cell apical/basal polarity / negative regulation of cell size / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / ERBB2 Regulates Cell Motility / 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 / 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 / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / wound healing, spreading of cells / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / positive regulation of cytokinesis / androgen receptor signaling pathway / cellular response to cytokine stimulus / cleavage furrow / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / 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 / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / regulation of cell migration / substrate adhesion-dependent cell spreading / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / G protein activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / ruffle membrane / neuron migration / positive regulation of protein serine/threonine kinase activity / cell morphogenesis / positive regulation of non-canonical NF-kappaB signal transduction / cytoplasmic side of plasma membrane / VEGFA-VEGFR2 Pathway / G beta:gamma signalling through PI3Kgamma / cell junction Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Longenecker, K. / Read, P. / Lin, S.-K. / Somlyo, A.P. / Nakamoto, R.K. / Derewenda, Z.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of a constitutively activated RhoA mutant (Q63L) at 1.55 A resolution. Authors: Longenecker, K. / Read, P. / Lin, S.K. / Somlyo, A.P. / Nakamoto, R.K. / Derewenda, Z.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kmq.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kmq.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kmq_validation.pdf.gz | 749.1 KB | Display | wwPDB validaton report |
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Full document | 1kmq_full_validation.pdf.gz | 752 KB | Display | |
Data in XML | 1kmq_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 1kmq_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/1kmq ftp://data.pdbj.org/pub/pdb/validation_reports/km/1kmq | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20646.635 Da / Num. of mol.: 1 / Mutation: Q63L, F25N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P61586 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GNP / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.38 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 282 K / Method: vapor diffusion / pH: 6.9 Details: PEG 8000, HEPES, dioxane, magnesium chloride, 2-mercaptoethanol, pH 6.9, VAPOR DIFFUSION, temperature 282K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K | ||||||||||||||||||||||||||||||
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: NSLS / Beamline: X9B / Wavelength: 0.9671 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9671 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. obs: 30966 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Redundancy: 5 % / Rsym value: 0.036 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.55→1.61 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.28 / % possible all: 84.6 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 97 % / Num. measured all: 154149 / Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 85 % / Rmerge(I) obs: 0.28 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→48 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.121 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.072 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.907 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20 /
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Software | *PLUS Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.19 / Rfactor Rwork: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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