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Yorodumi- PDB-5fr2: Farnesylated RhoA-GDP in complex with RhoGDI-alpha, lysine acetyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fr2 | ||||||
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Title | Farnesylated RhoA-GDP in complex with RhoGDI-alpha, lysine acetylated at K178 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / LYSINE-ACETYLATION / RHOA / RAS-SUPERFAMILY / RHOGDI / CYTOSKELETON / GDP | ||||||
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 / 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 / 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 / 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 / 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 / GTPase activator activity / 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 / 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: 3.35 Å | ||||||
Authors | Kuhlmann, N. / Wroblowski, S. / Knyphausen, P. / de Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Krueger, M. ...Kuhlmann, N. / Wroblowski, S. / Knyphausen, P. / de Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Krueger, M. / Schacherl, M. / Baumann, U. / James, L.C. / Chin, J.W. / Lammers, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural and Mechanistic Insights Into the Regulation of the Fundamental Rho-Regulator Rhogdi Alpha by Lysine Acetylation. Authors: Kuhlmann, N. / Wroblowski, S. / Knyphausen, P. / De Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Kruger, M. / Schacherl, M. / Baumann, U. / ...Authors: Kuhlmann, N. / Wroblowski, S. / Knyphausen, P. / De Boor, S. / Brenig, J. / Zienert, A.Y. / Meyer-Teschendorf, K. / Praefcke, G.J.K. / Nolte, H. / Kruger, M. / Schacherl, M. / Baumann, U. / James, L.C. / Chin, J.W. / Lammers, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fr2.cif.gz | 166.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fr2.ent.gz | 130.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/5fr2 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/5fr2 | HTTPS FTP |
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-Related structure data
Related structure data | 1doaS 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: 21943.287 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THIOESTER BETWEEN CYS190 AND FARNESYL-MOIETY / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61586 |
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#2: Protein | Mass: 24663.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: LYSINE-ACETYLATED AT K178 / Source: (gene. exp.) BOS TAURUS (cattle) / Plasmid: PCDF-DUET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19803 |
-Sugars , 1 types, 1 molecules
#6: Sugar | ChemComp-BGC / |
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-Non-polymers , 4 types, 20 molecules
#3: Chemical | ChemComp-FAR / |
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#4: Chemical | ChemComp-GDP / |
#5: Chemical | ChemComp-MG / |
#7: 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: 2.09 Å3/Da / Density % sol: 41.28 % / Description: NONE |
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Crystal grow | Details: 0.2 M LITHIUMSULFATE 0.1 M BIS-TRIS PH5.5 25% PEG3350 30% DEXTROSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 9, 2014 / Details: MIRRORS |
Radiation | Monochromator: BARTELS SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→44.24 Å / Num. obs: 17709 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.3 % / Biso Wilson estimate: 46.52 Å2 / Rmerge(I) obs: 0.52 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 3.35→3.62 Å / Redundancy: 15.7 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DOA Resolution: 3.35→44.245 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 24.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.35→44.245 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 67.9201 Å / Origin y: -55.5152 Å / Origin z: -19.6459 Å
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Refinement TLS group | Selection details: ALL |