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- PDB-4d1o: Structure of human endothelial nitric oxide synthase heme domain ... -

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Basic information

Entry
Database: PDB / ID: 4d1o
TitleStructure of human endothelial nitric oxide synthase heme domain with L-Arg bound
ComponentsNITRIC OXIDE SYNTHASE, ENDOTHELIAL
KeywordsOXIDOREDUCTASE / NITRIC OXIDE SYNTHASE
Function / homology
Function and homology information


NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / regulation of systemic arterial blood pressure by endothelin / response to fluid shear stress / pulmonary valve morphogenesis / negative regulation of biomineral tissue development / Nitric oxide stimulates guanylate cyclase ...NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / regulation of systemic arterial blood pressure by endothelin / response to fluid shear stress / pulmonary valve morphogenesis / negative regulation of biomineral tissue development / Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / aortic valve morphogenesis / tetrahydrobiopterin binding / arginine binding / positive regulation of Notch signaling pathway / endocardial cushion morphogenesis / blood vessel diameter maintenance / cadmium ion binding / removal of superoxide radicals / blood vessel remodeling / actin monomer binding / endothelial cell migration / homeostasis of number of cells within a tissue / negative regulation of platelet activation / positive regulation of blood vessel endothelial cell migration / nitric-oxide synthase (NADPH) / positive regulation of guanylate cyclase activity / eNOS activation / 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 / nitric oxide mediated signal transduction / vesicle membrane / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric-oxide synthase activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / mitochondrion organization / arginine catabolic process / response to hormone / nitric oxide biosynthetic process / VEGFR2 mediated vascular permeability / cell redox homeostasis / caveola / regulation of blood pressure / vasodilation / positive regulation of angiogenesis / FMN binding / Extra-nuclear estrogen signaling / flavin adenine dinucleotide binding / response to heat / NADP binding / response to lipopolysaccharide / endocytic vesicle membrane / calmodulin binding / cytoskeleton / oxidoreductase activity / Golgi membrane / negative regulation of cell population proliferation / heme binding / positive regulation of gene expression / Golgi apparatus / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric oxide synthase (NOS) signature. / Nitric oxide synthase, N-terminal / Nitric oxide synthase, oxygenase domain ...Nitric-oxide synthase, eukaryote / Nitric Oxide Synthase; Chain A, domain 3 / Nitric Oxide Synthase;Heme Domain; Chain A, domain 2 / Nitric Oxide Synthase; Chain A, domain 1 / Nitric Oxide Synthase; Chain A, domain 1 / Bovine Endothelial Nitric Oxide Synthase Heme Domain; Chain: A,domain 3 / Nitric Oxide Synthase;Heme Domain;Chain A domain 2 / Nitric oxide synthase (NOS) signature. / Nitric oxide synthase, N-terminal / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase, N-terminal domain superfamily / 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 / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Flavoprotein-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ARGININE / PROTOPORPHYRIN IX CONTAINING FE / 5,6,7,8-TETRAHYDROBIOPTERIN / GADOLINIUM ATOM / Nitric oxide synthase, endothelial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.819 Å
AuthorsLi, H. / Poulos, T.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structures of Human Constitutive Nitric Oxide Synthases
Authors: Li, H. / Jamal, J. / Plaza, C. / Pineda, S.H. / Chreifi, G. / Jing, Q. / Cinelli, M.A. / Silverman, R.B. / Poulos, T.L.
History
DepositionMay 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NITRIC OXIDE SYNTHASE, ENDOTHELIAL
B: NITRIC OXIDE SYNTHASE, ENDOTHELIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,36920
Polymers98,6922
Non-polymers3,67718
Water13,799766
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-138.2 kcal/mol
Surface area32400 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)62.395, 110.091, 153.322
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 / / CONSTITUTIVE NOS / CNOS / EC-NOS / ENDOTHELIAL NOS / ENOS / NOS TYPE III / NOSIII / CONSTITUTIVE ...CONSTITUTIVE NOS / CNOS / EC-NOS / ENDOTHELIAL NOS / ENOS / NOS TYPE III / NOSIII / CONSTITUTIVE NOS / NC-NOS / NOS TYPE I / NEURONAL NOS / N-NOS / NNOS / PEPTIDYL-CYSTEINE S-NITROSYLASE NOS1 / BNOS / NEURONAL NITRIC OXIDE SYNTHASE / NITRIC OXIDE SYNTHASE / BRAIN


Mass: 49345.770 Da / Num. of mol.: 2 / Fragment: RESIDUES 41-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29474, nitric-oxide synthase (NADPH)

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Non-polymers , 9 types, 784 molecules

#2: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: 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
#9: Chemical ChemComp-GD / GADOLINIUM ATOM


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.69 Å3/Da / Density % sol: 54.3 % / Description: RPIM 0.594 CC ONE HALF 0.533
Crystal growpH: 7.5
Details: 10-12% PEG3350, 0.1M BIS TRIS, PH7.5, 0.3M MG ACETATE, 0.1M GDCL3, 5 MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 95342 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.9
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 4 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NSE
Resolution: 1.819→48.392 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 18.62 / Stereochemistry target values: ML
Details: RESIDUES 110-118 IN CHAIN A AND 107-118 IN CHAIN B ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.192 4706 4.9 %
Rwork0.1548 --
obs0.1566 95245 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.819→48.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6409 0 229 766 7404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076923
X-RAY DIFFRACTIONf_angle_d1.1839512
X-RAY DIFFRACTIONf_dihedral_angle_d15.1492527
X-RAY DIFFRACTIONf_chiral_restr0.072982
X-RAY DIFFRACTIONf_plane_restr0.0051219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8186-1.83920.3741270.31612854X-RAY DIFFRACTION93
1.8392-1.86090.33141400.27282959X-RAY DIFFRACTION100
1.8609-1.88360.27471690.24362953X-RAY DIFFRACTION99
1.8836-1.90740.24921560.23432969X-RAY DIFFRACTION99
1.9074-1.93250.29151670.2152977X-RAY DIFFRACTION100
1.9325-1.9590.2541840.20092957X-RAY DIFFRACTION99
1.959-1.9870.24011540.18752985X-RAY DIFFRACTION100
1.987-2.01660.22011510.17983006X-RAY DIFFRACTION100
2.0166-2.04810.20951680.17072974X-RAY DIFFRACTION100
2.0481-2.08170.23311570.17373004X-RAY DIFFRACTION100
2.0817-2.11760.20621540.17042972X-RAY DIFFRACTION100
2.1176-2.15610.21571730.16853026X-RAY DIFFRACTION100
2.1561-2.19760.18651560.14872976X-RAY DIFFRACTION100
2.1976-2.24240.21361530.15193016X-RAY DIFFRACTION100
2.2424-2.29120.1961550.14683025X-RAY DIFFRACTION100
2.2912-2.34450.1951580.15292976X-RAY DIFFRACTION100
2.3445-2.40310.22461520.15023036X-RAY DIFFRACTION100
2.4031-2.46810.20971480.15483009X-RAY DIFFRACTION100
2.4681-2.54070.20731430.14753018X-RAY DIFFRACTION100
2.5407-2.62270.17711520.14653063X-RAY DIFFRACTION100
2.6227-2.71650.20281860.14692991X-RAY DIFFRACTION100
2.7165-2.82520.20791480.1543054X-RAY DIFFRACTION100
2.8252-2.95380.19421610.1523029X-RAY DIFFRACTION100
2.9538-3.10950.18991370.15463049X-RAY DIFFRACTION100
3.1095-3.30420.18581620.15173037X-RAY DIFFRACTION100
3.3042-3.55930.17521610.14513063X-RAY DIFFRACTION100
3.5593-3.91730.18541500.12433080X-RAY DIFFRACTION100
3.9173-4.48380.15631670.11993086X-RAY DIFFRACTION100
4.4838-5.64780.1351680.12613103X-RAY DIFFRACTION100
5.6478-48.40940.17661490.18313292X-RAY DIFFRACTION100
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)
10.09150.0311-0.05380.5595-0.12050.67110.0290.00250.05740.1421-0.01180.0129-0.0718-0.0354-0.00330.13940.00160.00340.1322-0.01040.122617.2053242.530932.0844
20.14630.1728-0.10470.8096-0.14980.40470.005-0.01130.0029-0.0922-0.0584-0.05590.07960.0058-0.07080.0906-0.00920.00870.11640.0170.108530.2571215.20899.8123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 68:480)
2X-RAY DIFFRACTION2(CHAIN B AND RESID 67:480)

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