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- PDB-3n61: Structure of neuronal nitric oxide synthase D597N/M336V mutant he... -

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Basic information

Entry
Database: PDB / ID: 3n61
TitleStructure of neuronal nitric oxide synthase D597N/M336V mutant heme domain in complex with 6,6'-(2,2'-(pyridine-3,5-diyl)bis(ethane-2,1-diyl))bis(4-methylpyridin-2-amine)
ComponentsNitric oxide synthase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / heme enzyme / nitric oxide synthase / substrate inhibitor / Zn binding' / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Nitric oxide stimulates guanylate cyclase / synaptic signaling by nitric oxide / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of hepatic stellate cell contraction / negative regulation of vasoconstriction / ROS and RNS production in phagocytes / negative regulation of iron ion transmembrane transport / Ion homeostasis / azurophil granule / retrograde trans-synaptic signaling by nitric oxide ...Nitric oxide stimulates guanylate cyclase / synaptic signaling by nitric oxide / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / negative regulation of hepatic stellate cell contraction / negative regulation of vasoconstriction / ROS and RNS production in phagocytes / negative regulation of iron ion transmembrane transport / Ion homeostasis / azurophil granule / retrograde trans-synaptic signaling by nitric oxide / negative regulation of cytosolic calcium ion concentration / response to nitric oxide / positive regulation of sodium ion transmembrane transport / postsynaptic specialization, intracellular component / positive regulation of the force of heart contraction / negative regulation of potassium ion transport / cadmium ion binding / regulation of heart contraction / negative regulation of serotonin uptake / multicellular organismal response to stress / regulation of sodium ion transport / calyx of Held / behavioral response to cocaine / striated muscle contraction / sodium channel regulator activity / peptidyl-cysteine S-nitrosylation / postsynaptic density, intracellular component / negative regulation of calcium ion transport / regulation of neurogenesis / negative regulation of hydrolase activity / negative regulation of insulin secretion / response to vitamin E / xenobiotic catabolic process => GO:0042178 / negative regulation of heart contraction / regulation of sensory perception of pain / nitric-oxide synthase (NADPH) / positive regulation of guanylate cyclase activity / negative regulation of blood pressure / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / T-tubule / nitric oxide mediated signal transduction / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / vesicle membrane / negative regulation of peptidyl-serine phosphorylation / nitric-oxide synthase activity / NADPH binding / arginine catabolic process / response to organonitrogen compound / positive regulation of histone acetylation / response to hormone / sarcoplasmic reticulum / nitric oxide biosynthetic process / response to nicotine / response to peptide hormone / muscle contraction / response to activity / cell periphery / response to nutrient levels / secretory granule / positive regulation of long-term synaptic potentiation / photoreceptor inner segment / sarcolemma / response to organic cyclic compound / response to lead ion / cellular response to growth factor stimulus / Z disc / phosphoprotein binding / female pregnancy / establishment of protein localization / vasodilation / calcium-dependent protein binding / positive regulation of neuron death / cellular response to mechanical stimulus / FMN binding / brain development / scaffold protein binding / flavin adenine dinucleotide binding / response to heat / NADP binding / transmembrane transporter binding / nuclear membrane / positive regulation of peptidyl-serine phosphorylation / response to lipopolysaccharide / ATPase binding / response to estrogen / response to ethanol / mitochondrial outer membrane / negative regulation of neuron apoptotic process / calmodulin binding / dendritic spine / postsynaptic density / response to hypoxia / aging / cytoskeleton / oxidoreductase activity / negative regulation of cell population proliferation / glutamatergic synapse / synapse / membrane raft
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, oxygenase domain ...Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / FAD binding domain / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ferredoxin reductase-type FAD binding domain profile. / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Riboflavin synthase-like beta-barrel / PDZ domain / Flavoprotein-like superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 5,6,7,8-TETRAHYDROBIOPTERIN / Chem-XFJ / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase, brain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsLi, H. / Delker, S.L. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2010
Title: Role of zinc in isoform-selective inhibitor binding to neuronal nitric oxide synthase .
Authors: Delker, S.L. / Xue, F. / Li, H. / Jamal, J. / Silverman, R.B. / Poulos, T.L.
History
DepositionMay 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitric oxide synthase
B: Nitric oxide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,42517
Polymers97,5592
Non-polymers2,86715
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-216 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)51.840, 110.500, 164.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nitric oxide synthase / / Endothelial NOS / eNOS / EC-NOS / NOS type III / NOSIII / Constitutive NOS / cNOS


Mass: 48779.477 Da / Num. of mol.: 2 / Mutation: D597N, M336V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NOS3 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29476, nitric-oxide synthase (NADPH)

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Non-polymers , 7 types, 418 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-XFJ / 6,6'-(pyridine-3,5-diyldiethane-2,1-diyl)bis(4-methylpyridin-2-amine)


Mass: 347.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25N5
#4: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN / Tetrahydrobiopterin


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 20-24% PEG3350 100mM MES 100-140mM ammonium acetate 5mM GSH, 35uM SDS, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2009 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 69511 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 21.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.504 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
CNSrefinement
Blu-IceIcedata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1OM4
Resolution: 1.95→38.49 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 9.01 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.141 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21323 3424 4.9 %RANDOM
Rwork0.17932 ---
obs0.18099 65998 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.227 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 187 403 7246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227097
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9929672
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7645828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11823.851335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.555151171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8071541
X-RAY DIFFRACTIONr_chiral_restr0.0950.2997
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215486
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6661.54105
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20826665
X-RAY DIFFRACTIONr_scbond_it1.98332992
X-RAY DIFFRACTIONr_scangle_it3.1724.53001
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.951→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 256 -
Rwork0.305 4751 -
obs-4751 98.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.4904-0.0188-0.3960.6115-0.38924.9288-0.06120.10680.0023-0.0117-0.02960.0229-0.0659-0.2760.09080.1257-0.0140.0060.1563-0.01810.020611.3574.7822.553
20.707-0.1812-0.16120.74260.33732.5235-0.0322-0.03260.0521-0.0517-0.03870.0006-0.0310.07140.07090.10580.0110.01880.11440.01750.019112.2574.7559.895
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A299 - 860
2X-RAY DIFFRACTION2B299 - 860

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