+Open data
-Basic information
Entry | Database: PDB / ID: 5fr1 | |||||||||
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Title | Double acetylated RhoGDI-alpha in complex with RhoA-GDP | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / RAS-SUPERFAMILY / GUANINE-NUCLEOTIDE-BINDING PROTEIN / MOLECULAR SWITCH / ACTIN-CYTOSKELETON RHOGDI-ALPHA / NUCLEOTIDE DISSOCIATION / PRENYLATION / LYSINE-ACETYLATION | |||||||||
Function / homology | Function and homology information Rho GDP-dissociation inhibitor 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 ...Rho GDP-dissociation inhibitor 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 / 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 / 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 / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / wound healing, spreading of cells / apical junction complex / regulation of neuron projection development / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / RHOC GTPase cycle / positive regulation of cytokinesis / androgen receptor signaling pathway / cerebral cortex cell migration / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / immunological synapse / 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 / regulation of cell migration / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / GTPase activator activity / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / G protein activity / kidney development / cell periphery / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / neuron migration / positive regulation of protein serine/threonine kinase activity / cell morphogenesis / cytoplasmic side of plasma membrane / ruffle membrane / VEGFA-VEGFR2 Pathway Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) BOS TAURUS (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | |||||||||
Authors | Kuhlmann, N. / Wroblowski, S. / Lammers, M. | |||||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Rhogdi Alpha Acetylation at K127 and K141 Affects Binding Towards Non-Prenylated Rhoa. Authors: Kuhlmann, N. / Wroblowski, S. / Scislowski, L. / Lammers, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fr1.cif.gz | 214.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fr1.ent.gz | 174.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fr1_validation.pdf.gz | 780.5 KB | Display | wwPDB validaton report |
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Full document | 5fr1_full_validation.pdf.gz | 786.2 KB | Display | |
Data in XML | 5fr1_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 5fr1_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/5fr1 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/5fr1 | HTTPS FTP |
-Related structure data
Related structure data | 1hh4S 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: 22000.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: GDP-BOUND / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61586 | ||||
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#2: Protein | Mass: 24704.752 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: LYSINE-ACETYLATED AT K127 AND K141 / Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19803 | ||||
#3: Chemical | ChemComp-GDP / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | LYSINE-ACETYLATED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.45 % / Description: NONE |
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Crystal grow | pH: 4.5 / Details: 4 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9791 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→60.11 Å / Num. obs: 11805 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 3 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HH4 Resolution: 2.75→60.11 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.893 / SU B: 27.465 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.309 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→60.11 Å
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Refine LS restraints |
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