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- PDB-2ll6: Solution NMR structure of CaM bound to iNOS CaM binding domain peptide -

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Basic information

Entry
Database: PDB / ID: 2ll6
TitleSolution NMR structure of CaM bound to iNOS CaM binding domain peptide
Components
  • Calmodulin
  • Nitric oxide synthase, inducible
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / : / establishment of protein localization to mitochondrial membrane / Nitric oxide stimulates guanylate cyclase / type 3 metabotropic glutamate receptor binding / prostaglandin secretion / positive regulation of killing of cells of another organism / ROS and RNS production in phagocytes / regulation of cellular respiration ...positive regulation of leukocyte mediated cytotoxicity / Inhibition of nitric oxide production / : / establishment of protein localization to mitochondrial membrane / Nitric oxide stimulates guanylate cyclase / type 3 metabotropic glutamate receptor binding / prostaglandin secretion / positive regulation of killing of cells of another organism / ROS and RNS production in phagocytes / regulation of cellular respiration / tetrahydrobiopterin binding / arginine binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / regulation of synaptic vesicle endocytosis / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / 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 / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / response to corticosterone / cortical cytoskeleton / superoxide metabolic process / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / regulation of cytokine production involved in inflammatory response / peptidyl-cysteine S-nitrosylation / protein phosphatase activator activity / RHO GTPases activate PAKs / regulation of insulin secretion / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / peroxisomal matrix / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / nitric-oxide synthase (NADPH) / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / nitric oxide mediated signal transduction / Protein methylation / nitric-oxide synthase activity / phosphatidylinositol 3-kinase binding / eNOS activation / arginine catabolic process / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of protein dephosphorylation / Ion homeostasis / regulation of calcium-mediated signaling / regulation of ryanodine-sensitive calcium-release channel activity / titin binding / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / nitric oxide biosynthetic process / activation of adenylate cyclase activity / substantia nigra development / adenylate cyclase activator activity / negative regulation of blood pressure / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere
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. / Sulfite reductase [NADPH] flavoprotein alpha-component-like, FAD-binding / NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain superfamily ...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. / 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, inducible / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsPiazza, M. / Futrega, K. / Spratt, D.E. / Dieckmann, T. / Guillemette, J.G.
CitationJournal: Biochemistry / Year: 2012
Title: Structure and Dynamics of Calmodulin (CaM) Bound to Nitric Oxide Synthase Peptides: Effects of a Phosphomimetic CaM Mutation.
Authors: Piazza, M. / Futrega, K. / Spratt, D.E. / Dieckmann, T. / Guillemette, J.G.
History
DepositionOct 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 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

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Assembly

Deposited unit
A: Calmodulin
B: Nitric oxide synthase, inducible


Theoretical massNumber of molelcules
Total (without water)18,6892
Polymers18,6892
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Nitric oxide synthase, inducible / Hepatocyte NOS / HEP-NOS / Inducible NO synthase / Inducible NOS / iNOS / NOS type II / Peptidyl- ...Hepatocyte NOS / HEP-NOS / Inducible NO synthase / Inducible NOS / iNOS / NOS type II / Peptidyl-cysteine S-nitrosylase NOS2


Mass: 1967.636 Da / Num. of mol.: 1 / Fragment: Calmodulin-binding region residues 515-531
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOS2, NOS2A / Production host: Escherichia coli (E. coli) / References: UniProt: P35228, nitric-oxide synthase (NADPH)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1313D CBCA(CO)NH
1423D CBCA(CO)NH
1513D HNCA
1613D HNCO
1713D HBHA(CO)NH
1823D HNCA
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11223D 1H-15N NOESY
11313D (H)CCH-COSY
11423D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-99% 13C; U-99% 15N] protein_1, 1.0 mM protein_2, 100 mM potassium chloride, 10 mM calcium chloride, 0.2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM protein_1, 1.0 mM [U-99% 13C; U-99% 15N] protein_2, 100 mM potassium chloride, 10 mM calcium chloride, 0.2 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMentity_1-1[U-99% 13C; U-99% 15N]1
1.0 mMentity_2-21
100 mMpotassium chloride-31
10 mMcalcium chloride-41
0.2 mMsodium azide-51
1.0 mMentity_1-62
1.0 mMentity_2-7[U-99% 13C; U-99% 15N]2
100 mMpotassium chloride-82
10 mMcalcium chloride-92
0.2 mMsodium azide-102
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX7002

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Processing

NMR software
NameDeveloperClassification
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
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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