+Open data
-Basic information
Entry | Database: PDB / ID: 3o0z | ||||||
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Title | Crystal structure of a coiled-coil domain from human ROCK I | ||||||
Components | Rho-associated protein kinase 1 | ||||||
Keywords | TRANSFERASE / coiled-coil | ||||||
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 / regulation of synapse maturation / bleb / positive regulation of amyloid-beta clearance / negative regulation of amyloid precursor protein catabolic process / neuron projection arborization / bleb assembly / embryonic morphogenesis / leukocyte tethering or rolling / negative regulation of biomineral tissue development / negative regulation of phosphorylation / actomyosin structure organization / aspartic-type endopeptidase inhibitor activity / regulation of establishment of endothelial barrier / RHO GTPases Activate ROCKs / negative regulation of motor neuron apoptotic process / regulation of stress fiber assembly / regulation of cell motility / Sema4D induced cell migration and growth-cone collapse / aortic valve morphogenesis / response to angiotensin / regulation of establishment of cell polarity / motor neuron apoptotic process / RHOBTB1 GTPase cycle / RND3 GTPase cycle / regulation of synaptic vesicle endocytosis / cortical actin cytoskeleton organization / regulation of neuron differentiation / regulation of focal adhesion assembly / leukocyte cell-cell adhesion / RHOB GTPase cycle / tau-protein kinase activity / leukocyte migration / negative regulation of amyloid-beta formation / EPHA-mediated growth cone collapse / mRNA destabilization / positive regulation of cardiac muscle hypertrophy / RHOC GTPase cycle / Apoptotic cleavage of cellular proteins / positive regulation of focal adhesion assembly / RHOH GTPase cycle / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / RHOA GTPase cycle / epithelial to mesenchymal transition / canonical NF-kappaB signal transduction / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / regulation of cell adhesion / regulation of cell migration / ruffle / EPHB-mediated forward signaling / centriole / blood vessel diameter maintenance / negative regulation of angiogenesis / negative regulation of protein binding / regulation of autophagy / protein localization to plasma membrane / regulation of actin cytoskeleton organization / tau protein binding / Schaffer collateral - CA1 synapse / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic stress granule / neuron projection development / G alpha (12/13) signalling events / lamellipodium / actin cytoskeleton organization / peptidyl-serine phosphorylation / secretory granule lumen / Potential therapeutics for SARS / positive regulation of MAPK cascade / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / positive regulation of gene expression / signal transduction / extracellular region / ATP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å | ||||||
Authors | Tu, D. / Eck, M.J. | ||||||
Citation | Journal: Plos One / Year: 2011 Title: Crystal Structure of a Coiled-Coil Domain from Human ROCK I. Authors: Tu, D. / Li, Y. / Song, H.K. / Toms, A.V. / Gould, C.J. / Ficarro, S.B. / Marto, J.A. / Goode, B.L. / Eck, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o0z.cif.gz | 263.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o0z.ent.gz | 228.3 KB | Display | PDB format |
PDBx/mmJSON format | 3o0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/3o0z ftp://data.pdbj.org/pub/pdb/validation_reports/o0/3o0z | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19893.670 Da / Num. of mol.: 4 / Fragment: coiled-coil domain (unp residues 535-700) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: Q13464, non-specific serine/threonine protein kinase #2: 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: 3.82 Å3/Da / Density % sol: 67.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: 13% MPD, 100 mM NaCl, 100 mM sodium acetate, 10 mM DTT, 5% glycerol, 10 mM spermidine, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97914 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2009 |
Radiation | Monochromator: MD2 microdiffractometers / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→50 Å / Num. all: 69169 / Num. obs: 69169 / % possible obs: 67.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 30.4 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 2.33→2.41 Å / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 13.2 / Num. unique all: 1487 / % possible all: 14.5 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.33→42.133 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 36.23 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.125 Å2 / ksol: 0.304 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.33→42.133 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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