+Open data
-Basic information
Entry | Database: PDB / ID: 1ftn | ||||||
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Title | CRYSTAL STRUCTURE OF THE HUMAN RHOA/GDP COMPLEX | ||||||
Components | TRANSFORMING PROTEIN RHOA (H12) | ||||||
Keywords | PROTO-ONCOGENE / GTP-BINDING / PRENYLATION / LIPOPROTEIN / SMALL P-PROTEIN | ||||||
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 / MIR, molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Wei, Y. / Zhang, Y. / Derewenda, U. / Liu, X. / Minor, W. / Nakamoto, R.K. / Somlyo, A.V. / Somlyo, A.P. / Derewenda, Z.S. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal structure of RhoA-GDP and its functional implications. Authors: Wei, Y. / Zhang, Y. / Derewenda, U. / Liu, X. / Minor, W. / Nakamoto, R.K. / Somlyo, A.V. / Somlyo, A.P. / 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 | 1ftn.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ftn.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ftn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ftn_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 1ftn_full_validation.pdf.gz | 462.1 KB | Display | |
Data in XML | 1ftn_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1ftn_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/1ftn ftp://data.pdbj.org/pub/pdb/validation_reports/ft/1ftn | 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: 21766.088 Da / Num. of mol.: 1 / Mutation: F25N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SYNTHETIC HUMAN RHOA GENE / Gene (production host): SYNTHETIC HUMAN RHOA GENE / Production host: Escherichia coli (E. coli) / References: UniProt: P61586 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GDP / |
#4: 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: 2.12 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.98 |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Dec 4, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→8 Å / Num. obs: 10913 / % possible obs: 97.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.08→2.15 Å / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 10.1 / % possible all: 81.1 |
Reflection | *PLUS Num. measured all: 40036 |
-Processing
Software |
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Refinement | Method to determine structure: MIR, molecular replacement Starting model: POLY ALANINE MODEL OF RAC1 Resolution: 2.1→8 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |