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Yorodumi- PDB-1s1c: Crystal structure of the complex between the human RhoA and Rho-b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s1c | ||||||
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Title | Crystal structure of the complex between the human RhoA and Rho-binding domain of human ROCKI | ||||||
Components |
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Keywords | SIGNALING PROTEIN / coiled-coil / GTPase / Rho kinase / ROCK | ||||||
Function / homology | Function and homology information regulation of amyloid-beta formation / regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / regulation of keratinocyte differentiation / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking ...regulation of amyloid-beta formation / regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / regulation of keratinocyte differentiation / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking / negative regulation of membrane protein ectodomain proteolysis / response to transforming growth factor beta / negative regulation of myosin-light-chain-phosphatase activity / regulation of cell junction assembly / positive regulation of dephosphorylation / negative regulation of bicellular tight junction assembly / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / regulation of synapse maturation / 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 / bleb / positive regulation of amyloid-beta clearance / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / neuron projection arborization / regulation of neural precursor cell proliferation / cleavage furrow formation / bleb assembly / embryonic morphogenesis / regulation of modification of postsynaptic actin cytoskeleton / leukocyte tethering or rolling / regulation of osteoblast proliferation / negative regulation of biomineral tissue development / negative regulation of phosphorylation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / actomyosin structure organization / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / aspartic-type endopeptidase inhibitor activity / regulation of establishment of endothelial barrier / 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 / regulation of stress fiber assembly / RHO GTPases activate CIT / regulation of cell motility / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / aortic valve morphogenesis / response to angiotensin / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / regulation of establishment of cell polarity / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / positive regulation of alpha-beta T cell differentiation / odontogenesis / motor neuron apoptotic process / RHOBTB1 GTPase cycle / wound healing, spreading of cells / PI3K/AKT activation / RND3 GTPase cycle / positive regulation of leukocyte adhesion to vascular endothelial cell / regulation of synaptic vesicle endocytosis / cortical actin cytoskeleton organization / apical junction complex / regulation of neuron differentiation / regulation of focal adhesion assembly / negative chemotaxis / leukocyte cell-cell adhesion / myosin binding / RHOB GTPase cycle / tau-protein kinase activity / leukocyte migration / negative regulation of amyloid-beta formation / EPHA-mediated growth cone collapse / mRNA destabilization / stress fiber assembly / regulation of neuron projection development Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Dvorsky, R. / Blumenstein, L. / Vetter, I.R. / Ahmadian, M.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural Insights into the Interaction of ROCKI with the Switch Regions of RhoA. Authors: Dvorsky, R. / Blumenstein, L. / Vetter, I.R. / Ahmadian, M.R. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE THAT TWO MOLECULES OF ROCKI (CHAINS X AND Y) REPRESENT BIOLOGICAL MOLECULE. IT CAN BIND IN SOLUTION EITHER ONE OR BOTH RHOA MOLECULES (CHAINS A AND B). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s1c.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s1c.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 1s1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/1s1c ftp://data.pdbj.org/pub/pdb/validation_reports/s1/1s1c | HTTPS FTP |
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-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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Details | ROCKI creates the dimer within asymmetric unit |
-Components
#1: Protein | Mass: 20611.588 Da / Num. of mol.: 2 / Fragment: RhoA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARHA, ARH12, RHOA, RHO12 / Production host: Escherichia coli (E. coli) / References: UniProt: P61586 #2: Protein | Mass: 8447.643 Da / Num. of mol.: 2 / Fragment: Rho-binding domain of ROCKI, residues 947-1015 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13464 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.5 Details: TRIS, PEG 3350, isopropyl alcohol, pH 7.5, EVAPORATION, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: ESRF / Beamline: ID29 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2001 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 17511 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5 / Biso Wilson estimate: 41.8 Å2 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 82.7 |
Reflection | *PLUS Num. measured all: 43736 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / % possible obs: 82.7 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 929385.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.482 Å2 / ksol: 0.37222 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.6 Å / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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