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- PDB-1niw: Crystal structure of endothelial nitric oxide synthase peptide bo... -

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Basic information

Entry
Database: PDB / ID: 1niw
TitleCrystal structure of endothelial nitric oxide synthase peptide bound to calmodulin
Components
  • Nitric-oxide synthase, endothelial
  • calmodulin
KeywordsSIGNALING 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 / 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 / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / cadmium ion binding / negative regulation of potassium ion transport / positive regulation of phosphoprotein phosphatase activity / negative regulation of calcium ion transport / adenylate cyclase binding / catalytic complex / actin monomer binding / calcium channel regulator activity / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of platelet activation / negative regulation of ryanodine-sensitive calcium-release channel activity / endothelial cell migration / nitric-oxide synthase (NADPH) / positive regulation of blood vessel endothelial cell migration / calcium channel inhibitor activity / cellular response to interferon-beta / blood vessel remodeling / positive regulation of DNA binding / nitric oxide mediated signal transduction / nitric-oxide synthase activity / phosphatidylinositol 3-kinase binding / eNOS activation / arginine catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / regulation of sodium ion transport / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / homeostasis of number of cells within a tissue / titin binding / lipopolysaccharide-mediated signaling pathway / potassium ion transmembrane transport / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / nitric oxide biosynthetic process / activation of adenylate cyclase activity / adenylate cyclase activator activity / negative regulation of blood pressure / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / removal of superoxide radicals / protein serine/threonine kinase activator activity / blood vessel diameter maintenance / mitochondrion organization / VEGFR2 mediated vascular permeability / regulation of cytokinesis / response to hormone / cell redox homeostasis / positive regulation of nitric-oxide synthase activity / caveola / establishment of localization in cell
Similarity search - Function
Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / EF-hand / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding ...Nitric-oxide synthase, eukaryote / Nitric oxide synthase, domain 2 superfamily / Nitric oxide synthase, domain 1 superfamily / Nitric oxide synthase, domain 3 superfamily / Nitric oxide synthase, N-terminal / Nitric oxide synthase, N-terminal domain superfamily / Nitric oxide synthase, oxygenase domain / Nitric oxide synthase (NOS) signature. / EF-hand / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily / FAD binding domain / Flavodoxin-like / Recoverin; domain 1 / 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 / Flavoprotein-like superfamily / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Nitric oxide synthase 3 / Calmodulin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsAoyagi, M. / Arvai, A.S. / Tainer, J.A. / Getzoff, E.D.
CitationJournal: 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
DepositionDec 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: calmodulin
B: Nitric-oxide synthase, endothelial
C: calmodulin
D: Nitric-oxide synthase, endothelial
E: calmodulin
F: Nitric-oxide synthase, endothelial
G: calmodulin
H: Nitric-oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,29429
Polymers77,3088
Non-polymers98621
Water4,738263
1
A: calmodulin
B: Nitric-oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5837
Polymers19,3272
Non-polymers2565
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-78 kcal/mol
Surface area8690 Å2
MethodPISA
2
C: calmodulin
D: Nitric-oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6118
Polymers19,3272
Non-polymers2846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-75 kcal/mol
Surface area8910 Å2
MethodPISA
3
E: calmodulin
F: Nitric-oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6118
Polymers19,3272
Non-polymers2846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-76 kcal/mol
Surface area8980 Å2
MethodPISA
4
G: calmodulin
H: Nitric-oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4876
Polymers19,3272
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-78 kcal/mol
Surface area8950 Å2
MethodPISA
5
A: calmodulin
B: Nitric-oxide synthase, endothelial
C: calmodulin
D: Nitric-oxide synthase, endothelial
hetero molecules

E: calmodulin
F: Nitric-oxide synthase, endothelial
G: calmodulin
H: Nitric-oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,29429
Polymers77,3088
Non-polymers98621
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area16780 Å2
ΔGint-327 kcal/mol
Surface area31050 Å2
MethodPISA
6
E: calmodulin
F: Nitric-oxide synthase, endothelial
hetero molecules

A: calmodulin
B: Nitric-oxide synthase, endothelial
hetero molecules

C: calmodulin
D: Nitric-oxide synthase, endothelial
hetero molecules

G: calmodulin
H: Nitric-oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,29429
Polymers77,3088
Non-polymers98621
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_746-x+2,y-1/2,-z+11
crystal symmetry operation2_747-x+2,y-1/2,-z+21
Buried area16080 Å2
ΔGint-327 kcal/mol
Surface area31760 Å2
MethodPISA
7
C: calmodulin
D: Nitric-oxide synthase, endothelial
hetero molecules

G: calmodulin
H: Nitric-oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,09914
Polymers38,6544
Non-polymers44510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area7590 Å2
ΔGint-164 kcal/mol
Surface area16370 Å2
MethodPISA
8
E: calmodulin
F: Nitric-oxide synthase, endothelial
hetero molecules

A: calmodulin
B: Nitric-oxide synthase, endothelial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,19515
Polymers38,6544
Non-polymers54111
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area7740 Å2
ΔGint-164 kcal/mol
Surface area16130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.521, 73.952, 71.142
Angle α, β, γ (deg.)90.00, 111.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ACEGBDFH

#1: Protein
calmodulin


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
Nitric-oxide synthase, endothelial / EC-NOS / NOS (type III) / NOSIII / Endothelial NOS / eNOS / Constitutive NOS / cNOS


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 / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.19 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
123 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
31 mMdithiothreitol1drop
45 mMpeptide1drop
55 mM1dropCaCl2
625-30 %(w/v)PEG80001reservoir
70.3-0.4 Mammonium sulfate1reservoirpH4.5-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979214, 0.979071, 0.911656
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792141
20.9790711
30.9116561
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2063 5 %RANDOM
Rwork0.223 ---
obs0.223 41186 99 %-
all-41624 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.0718 Å2 / ksol: 0.317885 e/Å3
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å26.28 Å2
2--2.21 Å20 Å2
3----4.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.05→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5164 0 37 263 5464
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.742
X-RAY DIFFRACTIONc_scbond_it2.392
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 -5.2 %
Rwork0.286 6429 -
obs--98.2 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.13
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69

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