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Yorodumi- PDB-1niw: Crystal structure of endothelial nitric oxide synthase peptide bo... -
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-Basic information
Entry | Database: PDB / ID: 1niw | ||||||
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Title | Crystal structure of endothelial nitric oxide synthase peptide bound to calmodulin | ||||||
Components |
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Keywords | SIGNALING PROTEIN/OXIDOREDUCTASE / Nitric oxide / calcium-binding protein / NOS / SIGNALING PROTEIN-OXIDOREDUCTASE COMPLEX | ||||||
Function / homology | Function and homology information regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / : / regulation of response to tumor cell ...regulation of store-operated calcium channel activity / regulation of high voltage-gated calcium channel activity / regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / : / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / response to fluid shear stress / ovulation from ovarian follicle / : / pulmonary valve morphogenesis / establishment of protein localization to mitochondrial membrane / negative regulation of biomineral tissue development / positive regulation of guanylate cyclase activity / Nitric oxide stimulates guanylate cyclase / type 3 metabotropic glutamate receptor binding / regulation of systemic arterial blood pressure by endothelin / ROS and RNS production in phagocytes / establishment of protein localization to membrane / tetrahydrobiopterin binding / presynaptic cytosol / aortic valve morphogenesis / arginine binding / regulation of synaptic vesicle endocytosis / negative regulation of high voltage-gated calcium channel activity / endocardial cushion morphogenesis / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / postsynaptic cytosol / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / ventricular septum morphogenesis / positive regulation of DNA binding / positive regulation of Notch signaling pathway / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / cadmium ion binding / negative regulation of potassium ion transport / : / negative regulation of calcium ion transport / adenylate cyclase binding / catalytic complex / actin monomer binding / detection of calcium ion / regulation of cardiac muscle contraction / calcium channel regulator activity / negative regulation of platelet activation / regulation of ryanodine-sensitive calcium-release channel activity / endothelial cell migration / nitric-oxide synthase (NADPH) / positive regulation of blood vessel endothelial cell migration / cellular response to interferon-beta / blood vessel remodeling / calcium channel inhibitor activity / nitric oxide mediated signal transduction / nitric-oxide synthase activity / phosphatidylinositol 3-kinase binding / eNOS activation / arginine catabolic process / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of sodium ion transport / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / titin binding / regulation of calcium-mediated signaling / lipopolysaccharide-mediated signaling pathway / homeostasis of number of cells within a tissue / voltage-gated potassium channel complex / sperm midpiece / potassium ion transmembrane transport / calcium channel complex / nitric oxide biosynthetic process / response to amphetamine / adenylate cyclase activator activity / negative regulation of blood pressure / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / removal of superoxide radicals / blood vessel diameter maintenance / protein serine/threonine kinase activator activity / potassium ion transport / negative regulation of smooth muscle cell proliferation / lung development / VEGFR2 mediated vascular permeability / response to hormone / cell redox homeostasis Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å | ||||||
Authors | Aoyagi, M. / Arvai, A.S. / Tainer, J.A. / Getzoff, E.D. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Structural basis for endothelial nitric oxide synthase binding to calmodulin Authors: Aoyagi, M. / Arvai, A.S. / Tainer, J.A. / Getzoff, E.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1niw.cif.gz | 145.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1niw.ent.gz | 123.1 KB | Display | PDB format |
PDBx/mmJSON format | 1niw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1niw_validation.pdf.gz | 514.2 KB | Display | wwPDB validaton report |
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Full document | 1niw_full_validation.pdf.gz | 537.3 KB | Display | |
Data in XML | 1niw_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 1niw_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/1niw ftp://data.pdbj.org/pub/pdb/validation_reports/ni/1niw | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 17143.406 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET9a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P62161, UniProt: P0DP29*PLUS #2: Protein/peptide | Mass: 2183.636 Da / Num. of mol.: 4 / Fragment: Calmodulin binding region / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide occurs naturally in Homo sapiens (human). References: UniProt: P29474, nitric-oxide synthase (NADPH) |
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-Non-polymers , 4 types, 284 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-EDO / #6: 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: 2.19 Å3/Da / Density % sol: 43.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5 Details: Polyethylene glycol, ammonium sulfate, pH 5, VAPOR DIFFUSION, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / 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: SSRL / Beamline: BL9-2 / Wavelength: 0.979214, 0.979071, 0.911656 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2001 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.05→30 Å / Num. obs: 41637 / % possible obs: 99.9 % / Observed criterion σ(I): 4 / Redundancy: 9.2 % / Biso Wilson estimate: 24.1 Å2 / Rsym value: 0.09 / Net I/σ(I): 26.6 | ||||||||||||
Reflection shell | Resolution: 2.05→2.12 Å / Mean I/σ(I) obs: 3.3 / Num. unique all: 4140 / Rsym value: 0.402 / % possible all: 99.9 | ||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 41626 / % possible obs: 99.7 % / Num. measured all: 129886 / Rmerge(I) obs: 0.06 | ||||||||||||
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.76 |
-Processing
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Refinement | Method to determine structure: MAD / Resolution: 2.05→19.78 Å / Rfactor Rfree error: 0.005 / 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: 42.0718 Å2 / ksol: 0.317885 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.222 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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