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- PDB-2o60: Calmodulin bound to peptide from neuronal nitric oxide synthase -

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Basic information

Entry
Database: PDB / ID: 2o60
TitleCalmodulin bound to peptide from neuronal nitric oxide synthase
Components
  • Calmodulin
  • Peptide corresponding to calmodulin binding domain of neuronal nitric oxide synthase
KeywordsMETAL BINDING PROTEIN / protein-peptide complex
Function / homology
Function and homology information


CH domain binding / Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / Ion homeostasis / negative regulation of hepatic stellate cell contraction / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide ...CH domain binding / Nitric oxide stimulates guanylate cyclase / ROS and RNS production in phagocytes / Ion homeostasis / negative regulation of hepatic stellate cell contraction / synaptic signaling by nitric oxide / negative regulation of iron ion transmembrane transport / azurophil granule / negative regulation of vasoconstriction / retrograde trans-synaptic signaling by nitric oxide / positive regulation of sodium ion transmembrane transport / postsynaptic specialization, intracellular component / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / myosin binding / negative regulation of cytosolic calcium ion concentration / negative regulation of peptidyl-serine phosphorylation / cadmium ion binding / positive regulation of the force of heart contraction / calyx of Held / negative regulation of potassium ion transport / behavioral response to cocaine / negative regulation of calcium ion transport / negative regulation of serotonin uptake / regulation of neurogenesis / nitric-oxide synthase (NADPH) / sodium channel regulator activity / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / negative regulation of insulin secretion / nitric oxide mediated signal transduction / nitric-oxide synthase activity / xenobiotic catabolic process / NADPH binding / arginine catabolic process / striated muscle contraction / enzyme regulator activity / regulation of sodium ion transport / T-tubule / sarcoplasmic reticulum membrane / cellular response to epinephrine stimulus / nitric oxide biosynthetic process / negative regulation of blood pressure / photoreceptor inner segment / response to hormone / secretory granule / positive regulation of long-term synaptic potentiation / muscle contraction / cell periphery / establishment of localization in cell / phosphoprotein binding / potassium ion transport / establishment of protein localization / sarcolemma / cellular response to growth factor stimulus / response to peptide hormone / Z disc / cellular response to mechanical stimulus / response to estrogen / vasodilation / calcium ion transport / calcium-dependent protein binding / disordered domain specific binding / FMN binding / NADP binding / flavin adenine dinucleotide binding / ATPase binding / scaffold protein binding / nuclear membrane / mitochondrial outer membrane / transmembrane transporter binding / negative regulation of neuron apoptotic process / response to lipopolysaccharide / dendritic spine / postsynaptic density / cytoskeleton / calmodulin binding / membrane raft / negative regulation of cell population proliferation / glutamatergic synapse / synapse / calcium ion binding / dendrite / heme binding / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
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 / PDZ domain / Flavoprotein-like superfamily / EF-hand domain pair / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / 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 / Nitric oxide synthase 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNg, H.L. / Alber, T. / Wand, A.J.
CitationJournal: To be Published
Title: Crystal structure of calmodulin-neuronal nitric oxide synthase complex
Authors: Valentine, K.G. / Ng, H.L. / Schneeweis, L. / Kranz, J.K. / Frederick, K.K. / Alber, T. / Wand, A.J.
History
DepositionDec 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Peptide in chain B is acetylated at N-terminus and amidated at C-terminus. ACE group was ...SEQUENCE Peptide in chain B is acetylated at N-terminus and amidated at C-terminus. ACE group was not modeled due to lack of electron density.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin
B: Peptide corresponding to calmodulin binding domain of neuronal nitric oxide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4656
Polymers19,3052
Non-polymers1604
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.126, 32.930, 73.830
Angle α, β, γ (deg.)90.00, 93.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CALM / Plasmid: pET 15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P62149
#2: Protein/peptide Peptide corresponding to calmodulin binding domain of neuronal nitric oxide synthase


Mass: 2583.192 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. This sequence occurs naturally in mice. Peptide is acetylated at N-terminus and amidated at C-terminus.
References: UniProt: Q9Z0J4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG 4000, 0.2 M sodium acetate, 0.1 M sodium citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.55→74.536 Å / Num. obs: 23547 / Redundancy: 3.6 % / Rsym value: 0.039 / Net I/σ(I): 18.1
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.254

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
Blu-IceIcedata collection
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→74.54 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.231 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24375 1208 5.1 %RANDOM
Rwork0.20162 ---
obs0.20378 22393 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.633 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.47 Å2
2--0.3 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.55→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 4 165 1485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221357
X-RAY DIFFRACTIONr_bond_other_d0.0020.02922
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9741812
X-RAY DIFFRACTIONr_angle_other_deg1.50532279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1185166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.06126.57573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56915275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.492156
X-RAY DIFFRACTIONr_chiral_restr0.0950.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02248
X-RAY DIFFRACTIONr_nbd_refined0.2490.2377
X-RAY DIFFRACTIONr_nbd_other0.1790.2971
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2701
X-RAY DIFFRACTIONr_nbtor_other0.090.2642
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2111
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.120.213
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.191.5870
X-RAY DIFFRACTIONr_mcbond_other0.3761.5345
X-RAY DIFFRACTIONr_mcangle_it1.65921332
X-RAY DIFFRACTIONr_scbond_it2.4623549
X-RAY DIFFRACTIONr_scangle_it3.4734.5480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 80 -
Rwork0.205 1673 -
obs--99.89 %
Refinement TLS params.

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

IDL11 (°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)
112.86868.0799-5.2614.5695-6.39358.08210.20160.08980.4498-0.17860.08320.3548-0.2114-0.1296-0.2848-0.2411-0.00210.0124-0.2256-0.05-0.115237.860527.54623.868
24.53540.8993-0.48721.5874-0.47742.71730.0779-0.3399-0.11870.1246-0.08910.00390.03550.0010.0112-0.2202-0.02810.0034-0.23540.0054-0.212722.966714.95147.7495
31.3376-1.48010.71776.23744.84299.4696-0.0284-0.3325-0.39570.0669-0.26930.25350.19-0.80380.2977-0.0884-0.0480.01440.0647-0.034-0.169925.545923.910828.5946
42.70540.70191.78224.19562.45348.4771-0.0811-0.0398-0.0107-0.46310.0496-0.2544-0.53910.2320.0316-0.0073-0.05410.00650.0310.0134-0.19233.894230.073925.8521
513.92033.58568.93986.11581.594810.772-0.1140.51080.1643-0.165-0.0512-0.3938-0.24750.8270.1651-0.1412-0.04630.0187-0.1187-0.0359-0.176428.07825.861816.2411
623.94578.9513-3.899618.5589-7.287112.8341-0.2377-0.58910.78421.1991-0.09521.7203-0.6701-0.72660.3329-0.08560.0031-0.0206-0.1145-0.0858-0.109714.837623.960812.8067
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 14
2X-RAY DIFFRACTION2A15 - 74
3X-RAY DIFFRACTION2A402 - 403
4X-RAY DIFFRACTION3A87 - 113
5X-RAY DIFFRACTION3A404
6X-RAY DIFFRACTION4A114 - 148
7X-RAY DIFFRACTION4A401
8X-RAY DIFFRACTION5B4 - 18
9X-RAY DIFFRACTION6B19 - 23

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