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- PDB-2n8j: Structure and 15N relaxation data of Calmodulin bound to the endo... -

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Basic information

Entry
Database: PDB / ID: 2n8j
TitleStructure and 15N relaxation data of Calmodulin bound to the endothelial Nitric Oxide Synthase Calmodulin Binding Domain Peptide at Physiological Calcium Concentration
Components
  • Calmodulin
  • Nitric oxide synthase, endothelial
KeywordsPROTEIN BINDING / Calmodulin / Nitric Oxide Synthase / eNOS / Dynamics / Order parameters
Function / homology
Function and homology information


regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / negative regulation of muscle hyperplasia / tetrahydrobiopterin metabolic process / NOSTRIN mediated eNOS trafficking / smooth muscle hyperplasia / regulation of nervous system process / : / : / : ...regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / negative regulation of muscle hyperplasia / tetrahydrobiopterin metabolic process / NOSTRIN mediated eNOS trafficking / smooth muscle hyperplasia / regulation of nervous system process / : / : / : / : / superoxide-generating NAD(P)H oxidase activity / : / positive regulation of protein autophosphorylation / ovulation from ovarian follicle / pulmonary valve morphogenesis / negative regulation of peptidyl-threonine phosphorylation / response to fluid shear stress / negative regulation of biomineral tissue development / Nitric oxide stimulates guanylate cyclase / : / regulation of systemic arterial blood pressure by endothelin / type 3 metabotropic glutamate receptor binding / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / aortic valve morphogenesis / arginine binding / positive regulation of peptidyl-threonine phosphorylation / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / endocardial cushion morphogenesis / Calmodulin induced events / positive regulation of DNA binding / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / response to corticosterone / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / PKA activation / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / ventricular septum morphogenesis / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / positive regulation of Notch signaling pathway / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / nitric-oxide synthase binding / presynaptic endocytosis / regulation of synaptic vesicle exocytosis / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / cadmium ion binding / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of calcium ion transport / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / negative regulation of potassium ion transport / Ion transport by P-type ATPases / adenylate cyclase binding / Uptake and function of anthrax toxins / negative regulation of platelet activation / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / actin monomer binding / positive regulation of protein serine/threonine kinase activity / positive regulation of blood vessel endothelial cell migration / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / nitric oxide mediated signal transduction / blood vessel remodeling / DARPP-32 events / nitric-oxide synthase (NADPH) / Smooth Muscle Contraction / regulation of synaptic vesicle endocytosis / detection of calcium ion / regulation of cardiac muscle contraction / nitric-oxide synthase activity / endothelial cell migration / catalytic complex / RHO GTPases activate IQGAPs / L-arginine catabolic process / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / activation of adenylate cyclase activity / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / cellular response to interferon-beta / Activation of AMPK downstream of NMDARs / presynaptic cytosol
Similarity search - Function
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 ...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 / 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
Similarity search - Domain/homology
Calmodulin-1 / Nitric oxide synthase 3 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsPiazza, M. / Guillemette, G. / Dieckmann, T.
CitationJournal: Biochemistry / Year: 2016
Title: Structural Studies of a Complex Between Endothelial Nitric Oxide Synthase and Calmodulin at Physiological Calcium Concentration.
Authors: Piazza, M. / Dieckmann, T. / Guillemette, J.G.
History
DepositionOct 16, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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


Theoretical massNumber of molelcules
Total (without water)19,1072
Polymers19,1072
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-16 kcal/mol
Surface area10420 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1minimized average structure

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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.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Nitric oxide synthase, endothelial / Constitutive NOS / cNOS / EC-NOS / Endothelial NOS / eNOS / NOS type III / NOSIII


Mass: 2385.844 Da / Num. of mol.: 1 / Fragment: UNP residues 491-512 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P29474

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCA
1413D (H)CCH-TOCSY
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliphatic
1712D 1H-1H edited filtered NOESY

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] CaM, 1 mM eNOS, 100 mM potassium chloride, 30 mM MOPS, 4 mM EGTA, 6 mM CaEGTA, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCaM-1[U-99% 13C; U-99% 15N]1
1 mMeNOS-21
100 mMpotassium chloride-31
30 mMMOPS-41
4 mMEGTA-51
6 mMCaEGTA-61
Sample conditionsIonic strength: 0.15 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2959
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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