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- PDB-3hsn: Ternary structure of neuronal nitric oxide synthase with NHA and ... -

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Basic information

Entry
Database: PDB / ID: 3hsn
TitleTernary structure of neuronal nitric oxide synthase with NHA and CO bound
ComponentsNitric oxide synthase, brain
KeywordsOXIDOREDUCTASE / nitric oxide synthase / heme enzyme / diatomic ligand / Calmodulin-binding / Cell membrane / Cell projection / FAD / FMN / Heme / Iron / Membrane / Metal-binding / NADP
Function / homology
Function and homology information


negative regulation of hepatic stellate cell contraction / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / response to vitamin B3 / azurophil granule / postsynaptic specialization, intracellular component / negative regulation of vasoconstriction ...negative regulation of hepatic stellate cell contraction / Nitric oxide stimulates guanylate cyclase / positive regulation of adenylate cyclase-activating adrenergic receptor signaling pathway / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / ROS and RNS production in phagocytes / response to vitamin B3 / azurophil granule / postsynaptic specialization, intracellular component / negative regulation of vasoconstriction / negative regulation of cytosolic calcium ion concentration / Ion homeostasis / response to nitric oxide / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of sodium ion transmembrane transport / peptidyl-cysteine S-nitrosylase activity / regulation of postsynaptic membrane potential / cadmium ion binding / positive regulation of the force of heart contraction / behavioral response to cocaine / negative regulation of potassium ion transport / negative regulation of calcium ion transport / regulation of neurogenesis / nitric oxide mediated signal transduction / nitric-oxide synthase (NADPH) / sodium channel regulator activity / negative regulation of serotonin uptake / response to vitamin E / postsynaptic density, intracellular component / nitric-oxide synthase activity / multicellular organismal response to stress / xenobiotic catabolic process / L-arginine catabolic process / negative regulation of insulin secretion / NADPH binding / striated muscle contraction / regulation of sodium ion transport / nitric oxide-cGMP-mediated signaling / nitric oxide metabolic process / negative regulation of blood pressure / response to hormone / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / photoreceptor inner segment / T-tubule / nitric oxide biosynthetic process / calyx of Held / secretory granule / sarcoplasmic reticulum / positive regulation of long-term synaptic potentiation / response to activity / cell periphery / female pregnancy / establishment of localization in cell / phosphoprotein binding / response to nicotine / establishment of protein localization / response to lead ion / response to nutrient levels / potassium ion transport / : / sarcolemma / cellular response to growth factor stimulus / caveola / response to peptide hormone / Z disc / response to estrogen / cellular response to mechanical stimulus / calcium ion transport / calcium-dependent protein binding / vasodilation / FMN binding / flavin adenine dinucleotide binding / NADP binding / ATPase binding / response to heat / scaffold protein binding / nuclear membrane / dendritic spine / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / cytoskeleton / response to hypoxia / calmodulin binding / postsynaptic density / membrane raft / negative regulation of cell population proliferation / synapse / heme binding / dendrite / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex
Similarity search - Function
Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / 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, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily ...Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase; Chain A, domain 1 / 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, eukaryote / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / : / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Flavoprotein pyridine nucleotide cytochrome reductase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / 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 / CARBON MONOXIDE / 5,6,7,8-TETRAHYDROBIOPTERIN / N-OMEGA-HYDROXY-L-ARGININE / PROTOPORPHYRIN IX CONTAINING FE / Nitric oxide synthase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.91 Å
AuthorsDoukov, T. / Li, H. / Soltis, M. / Poulos, T.L.
CitationJournal: Biochemistry / Year: 2009
Title: Single crystal structural and absorption spectral characterizations of nitric oxide synthase complexed with N(omega)-hydroxy-L-arginine and diatomic ligands.
Authors: Doukov, T. / Li, H. / Soltis, M. / Poulos, T.L.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)100,60520
Polymers97,6252
Non-polymers2,98018
Water9,728540
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11990 Å2
ΔGint-88 kcal/mol
Surface area33070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.160, 110.847, 165.042
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, brain / BNOS / NOS type I / Neuronal NOS / N-NOS / nNOS / Constitutive NOS / NC-NOS


Mass: 48812.527 Da / Num. of mol.: 2 / Fragment: UNP residues 297-718
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nos1, Bnos / 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 , 8 types, 558 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-H4B / 5,6,7,8-TETRAHYDROBIOPTERIN


Mass: 241.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N5O3 / Comment: neurotransmitter*YM
#5: Chemical ChemComp-HAR / N-OMEGA-HYDROXY-L-ARGININE


Type: L-peptide linking / Mass: 190.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14N4O3
#6: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 278 K / pH: 5.8
Details: PEG3350, MES, ammonium acetate SDS, GSH, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2006 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. obs: 73350 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 12.7
Reflection shellResolution: 1.91→2.02 Å / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.496 / % possible all: 91.8

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Processing

Software
NameClassification
PHENIXrefinement
REFMACrefinement
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1LZX

1lzx


Resolution: 1.91→44.09 Å / SU ML: 0.25 / Isotropic thermal model: isotropic / σ(F): 1.99 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.21 3717 5.07 %
Rwork0.167 --
obs0.169 73249 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.55 Å2 / ksol: 0.39 e/Å3
Refine analyzeLuzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.91→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6703 0 201 540 7444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117146
X-RAY DIFFRACTIONf_angle_d1.389720
X-RAY DIFFRACTIONf_dihedral_angle_d18.9132589
X-RAY DIFFRACTIONf_chiral_restr0.0881007
X-RAY DIFFRACTIONf_plane_restr0.0061231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.93120.34541290.28532334X-RAY DIFFRACTION88
1.9312-1.95660.33621160.27242444X-RAY DIFFRACTION93
1.9566-1.98340.30221390.24842400X-RAY DIFFRACTION92
1.9834-2.01180.28891210.23742510X-RAY DIFFRACTION94
2.0118-2.04180.25741260.2142439X-RAY DIFFRACTION94
2.0418-2.07370.25631620.20572460X-RAY DIFFRACTION94
2.0737-2.10770.25821340.20542465X-RAY DIFFRACTION95
2.1077-2.1440.2581320.20942533X-RAY DIFFRACTION96
2.144-2.1830.27091340.19822534X-RAY DIFFRACTION97
2.183-2.2250.24131390.19272530X-RAY DIFFRACTION97
2.225-2.27040.25081300.192617X-RAY DIFFRACTION98
2.2704-2.31980.24521470.18032529X-RAY DIFFRACTION98
2.3198-2.37370.23311360.17242622X-RAY DIFFRACTION98
2.3737-2.43310.23041330.1692567X-RAY DIFFRACTION99
2.4331-2.49890.19511390.17052661X-RAY DIFFRACTION99
2.4989-2.57240.21651430.15912599X-RAY DIFFRACTION99
2.5724-2.65540.1891070.16332655X-RAY DIFFRACTION99
2.6554-2.75030.20061410.16352655X-RAY DIFFRACTION99
2.7503-2.86040.20691370.15782613X-RAY DIFFRACTION99
2.8604-2.99060.22581660.15842599X-RAY DIFFRACTION99
2.9906-3.14820.25221200.16542645X-RAY DIFFRACTION99
3.1482-3.34540.16511320.15472643X-RAY DIFFRACTION99
3.3454-3.60360.1731440.13772675X-RAY DIFFRACTION99
3.6036-3.9660.17331460.1332640X-RAY DIFFRACTION99
3.966-4.53940.18161510.12642655X-RAY DIFFRACTION98
4.5394-5.71720.16271520.14462705X-RAY DIFFRACTION99
5.7172-44.10250.20041610.1762803X-RAY DIFFRACTION97
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.1205-0.0199-0.33730.4597-0.13083.3787-0.05430.0821-0.01290.0133-0.03410.0005-0.0173-0.27830.00020.0604-0.0191-0.00030.095-0.00650.105912.09774.913659.9481
20.3226-0.1363-0.17730.46530.25391.5118-0.0185-0.03950.0322-0.0458-0.03780.01510.02080.00900.05910.01350.01520.08950.00320.1347
Refinement TLS groupSelection details: CHAIN B

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