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- PDB-8dgh: NMR Structure of calmodulin bound to C-terminal site in the beta-... -

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Basic information

Entry
Database: PDB / ID: 8dgh
TitleNMR Structure of calmodulin bound to C-terminal site in the beta-subunit of cyclic nucleotide-gated channel
Components
  • Calmodulin-1
  • Cyclic nucleotide-gated cation channel beta-1
KeywordsMETAL BINDING PROTEIN / retina / CNGB1 / phototransduction
Function / homology
Function and homology information


olfactory nerve maturation / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / protein localization to organelle / detection of light stimulus involved in visual perception / ion channel modulating, G protein-coupled receptor signaling pathway / response to odorant / VxPx cargo-targeting to cilium / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity ...olfactory nerve maturation / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / protein localization to organelle / detection of light stimulus involved in visual perception / ion channel modulating, G protein-coupled receptor signaling pathway / response to odorant / VxPx cargo-targeting to cilium / intracellular cyclic nucleotide activated cation channel complex / intracellularly cGMP-activated cation channel activity / Golgi-associated vesicle membrane / intracellularly cAMP-activated cation channel activity / photoreceptor cell maintenance / retina homeostasis / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / ciliary membrane / 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 / positive regulation of cyclic-nucleotide phosphodiesterase activity / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / 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 / 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 / monoatomic cation transmembrane transport / protein phosphatase activator activity / monoatomic cation transport / RHO GTPases activate PAKs / membrane depolarization / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / ligand-gated monoatomic ion channel activity / Long-term potentiation / phototransduction / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / cGMP binding / regulation of cardiac muscle contraction / photoreceptor outer segment / negative regulation of ryanodine-sensitive calcium-release channel activity / transmembrane transporter complex / Smooth Muscle Contraction / calcium channel inhibitor activity / RHO GTPases activate IQGAPs / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cAMP binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / Ion homeostasis / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated potassium channel complex / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / regulation of cytosolic calcium ion concentration / substantia nigra development / adenylate cyclase activator activity / visual perception / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane
Similarity search - Function
Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / EF-hand domain pair ...Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / 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 / Cyclic nucleotide-gated channel beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBej, A. / Ames, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY012347 United States
CitationJournal: Biochemistry / Year: 2022
Title: NMR Structures of Calmodulin Bound to Two Separate Regulatory Sites in the Retinal Cyclic Nucleotide-Gated Channel.
Authors: Bej, A. / Ames, J.B.
History
DepositionJun 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1May 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-1
B: Cyclic nucleotide-gated cation channel beta-1


Theoretical massNumber of molelcules
Total (without water)18,3052
Polymers18,3052
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area940 Å2
ΔGint-8 kcal/mol
Surface area5510 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP23
#2: Protein/peptide Cyclic nucleotide-gated cation channel beta-1 / Cyclic nucleotide-gated cation channel 4 / CNG channel 4 / CNG-4 / CNG4 / Cyclic nucleotide-gated ...Cyclic nucleotide-gated cation channel 4 / CNG channel 4 / CNG-4 / CNG4 / Cyclic nucleotide-gated cation channel gamma / Cyclic nucleotide-gated cation channel modulatory subunit / Cyclic nucleotide-gated channel beta-1 / CNG channel beta-1 / Glutamic acid-rich protein / GARP


Mass: 1452.810 Da / Num. of mol.: 1 / Fragment: C-terminal site, residues 1128-1139 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14028

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D HBHANH
191isotropic13D HBHA(CO)NH
181isotropic13D C(CO)NH
171isotropic13D H(CCO)NH
162isotropic12D 1H-13C HSQC
1112isotropic13D (H)CCH-TOCSY
1102isotropic13D 1H-13C NOESY
1131isotropic12D 1H-13C HSQC aromatic
1122isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.4 mM [U-100% 13C; U-100% 15N] Calmodulin, 1.2 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride, 90% H2O/10% D2O13C_15N_Sample_in_H2O90% H2O/10% D2O
solution20.4 mM [U-100% 13C; U-100% 15N] Calmodulin, 1.2 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride, 100% D2O13C_15N_Sample_in_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMCalmodulin[U-100% 13C; U-100% 15N]1
1.2 mMCyclic nucleotide-gated cation channel beta-1natural abundance1
20 mMTRIS[U-100% 2H]1
1 mMCalcium chloridenatural abundance1
0.4 mMCalmodulin[U-100% 13C; U-100% 15N]2
1.2 mMCyclic nucleotide-gated cation channel beta-1natural abundance2
20 mMTRIS[U-100% 2H]2
1 mMCalcium chloridenatural abundance2
Sample conditionsIonic strength: 1 mM / Label: Condition_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
HADDOCKBonvinrefinement
HADDOCKBonvinstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 3
Details: The authors state that for the structure of the calmodulin C-lobe, they used residues 82-149 from the available structure of the calmodulin/IQ domain complex (PDB ID - 2F3Y, chain A). The ...Details: The authors state that for the structure of the calmodulin C-lobe, they used residues 82-149 from the available structure of the calmodulin/IQ domain complex (PDB ID - 2F3Y, chain A). The structure of the peptide fragment of the Cyclic nucleotide-gated cation channel beta-1 was generated in Modeller 9.25 using the template of creatine kinase peptide (PDB ID - 7BF2, chain B[auth DDD]). Finally, the HADDOCK calculation was performed on an energy minimized peptide obtained after energy minimization in Gromacs.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 200 / Conformers submitted total number: 10

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