+Open data
-Basic information
Entry | Database: PDB / ID: 3hr4 | ||||||
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Title | Human iNOS Reductase and Calmodulin Complex | ||||||
Components |
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Keywords | Oxidoreductase/METAL BINDING PROTEIN / inducible nitric oxide synthase / NOS / iNOS / calmodulin / Calmodulin-binding / FAD / FMN / Heme / Iron / Metal-binding / NADP / Oxidoreductase / Phosphoprotein / Isopeptide bond / Methylation / Oxidoreductase-METAL BINDING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / : / establishment of protein localization to mitochondrial membrane / Nitric oxide stimulates guanylate cyclase / type 3 metabotropic glutamate receptor binding / positive regulation of killing of cells of another organism / prostaglandin secretion / ROS and RNS production in phagocytes / regulation of cellular respiration ...positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / : / establishment of protein localization to mitochondrial membrane / Nitric oxide stimulates guanylate cyclase / type 3 metabotropic glutamate receptor binding / positive regulation of killing of cells of another organism / prostaglandin secretion / ROS and RNS production in phagocytes / regulation of cellular respiration / tetrahydrobiopterin binding / arginine binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / 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 / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / response to corticosterone / positive regulation of DNA binding / cortical cytoskeleton / superoxide metabolic process / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / peptidyl-cysteine S-nitrosylation / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cytokine production involved in inflammatory response / protein phosphatase activator activity / RHO GTPases activate PAKs / : / regulation of insulin secretion / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / peroxisomal matrix / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / nitric-oxide synthase (NADPH) / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / nitric oxide mediated signal transduction / nitric-oxide synthase activity / Protein methylation / 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 / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / nitric oxide biosynthetic process / response to amphetamine / substantia nigra development / adenylate cyclase activator activity / negative regulation of blood pressure / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Xia, C. / Misra, I. / Iyanaki, T. / Kim, J.J.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Regulation of Interdomain Interactions by CaM in Inducible Nitric Oxide Synthase Authors: Xia, C. / Misra, I. / Iyanaki, T. / Kim, J.J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hr4.cif.gz | 280.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hr4.ent.gz | 222.3 KB | Display | PDB format |
PDBx/mmJSON format | 3hr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hr4_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 3hr4_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3hr4_validation.xml.gz | 59.5 KB | Display | |
Data in CIF | 3hr4_validation.cif.gz | 78.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/3hr4 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/3hr4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 25045.004 Da / Num. of mol.: 4 / Fragment: Residues 503-715 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: Calmodulin, Inducible Nitric Oxide Synthase, NOS2, NOS2A Plasmid: PCWORI+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P35228, nitric-oxide synthase (NADPH) #2: Protein | Mass: 16852.545 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII Plasmid: pKK-CaM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62158, UniProt: P0DP23*PLUS #3: Chemical | ChemComp-FMN / #4: Chemical | ChemComp-CA / #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: 2.24 Å3/Da / Density % sol: 45.19 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 8K, SODIUM ACETATE, SODIUM CHLORATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 27, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.69 Å / Num. obs: 48283 / % possible obs: 94.6 % / Redundancy: 2.7 % / Biso Wilson estimate: 60.9 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TLL, 1NIW, 1FOT Resolution: 2.5→29.69 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 428243.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.8557 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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