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- PDB-8dgk: NMR structure of calmodulin bound to N-terminal site in the beta-... -

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Basic information

Entry
Database: PDB / ID: 8dgk
TitleNMR structure of calmodulin bound to N-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 / non-motile cilium membrane / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / protein localization to organelle / intracellular cyclic nucleotide activated cation channel complex / detection of light stimulus involved in visual perception / intracellularly cGMP-activated cation channel activity / ion channel modulating, G protein-coupled receptor signaling pathway / response to odorant ...olfactory nerve maturation / non-motile cilium membrane / detection of chemical stimulus involved in sensory perception of smell / photoreceptor cell outer segment organization / protein localization to organelle / intracellular cyclic nucleotide activated cation channel complex / detection of light stimulus involved in visual perception / intracellularly cGMP-activated cation channel activity / ion channel modulating, G protein-coupled receptor signaling pathway / response to odorant / VxPx cargo-targeting to cilium / rod photoreceptor outer segment / intracellularly cAMP-activated cation channel activity / Golgi-associated vesicle membrane / photoreceptor cell maintenance / retina homeostasis / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / sodium channel activity / 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 / ciliary membrane / 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 / autophagosome membrane docking / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / sodium ion transport / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Synthesis of IP3 and IP4 in the cytosol / negative regulation of peptidyl-threonine phosphorylation / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / monoatomic cation transmembrane transport / RHO GTPases activate PAKs / monoatomic cation transport / Ion transport by P-type ATPases / : / membrane depolarization / Uptake and function of anthrax toxins / phototransduction / cGMP binding / Long-term potentiation / Regulation of MECP2 expression and activity / ligand-gated monoatomic ion channel activity / Calcineurin activates NFAT / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / photoreceptor outer segment / Smooth Muscle Contraction / transmembrane transporter complex / regulation of ryanodine-sensitive calcium-release channel activity / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / cellular response to interferon-beta / eNOS activation / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / cAMP binding / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / : / titin binding / positive regulation of protein autophosphorylation / regulation of calcium-mediated signaling / sperm midpiece / regulation of cytosolic calcium ion concentration / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / sarcomere / visual perception / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated vascular permeability
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 ...: / 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

Downloads & links

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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)18,3582
Polymers18,3582
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1160 Å2
ΔGint-13 kcal/mol
Surface area6210 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: 1505.780 Da / Num. of mol.: 1 / Fragment: N-terminal site, residues 565-576 / 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 HNCO
131isotropic23D HNCA
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
1151isotropic13D HBHA(CO)NH
1141isotropic23D HBHANH
1131isotropic23D C(CO)NH
1121isotropic23D H(CCO)NH
1112isotropic22D 1H-13C HSQC
1103isotropic12D 1H-13C HSQC
192isotropic13D (H)CCH-TOCSY
182isotropic23D 1H-13C NOESY
172isotropic22D 1H-13C HSQC aromatic
162isotropic12D 1H-1H NOESY
1162isotropic22D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride, 90% H2O/10% D2O13C_15N_Sample_H2O90% H2O/10% D2O
solution20.5 mM [U-100% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride, 100% D2O13C_15N_Sample_D2O100% D2O
solution30.5 mM [U-10% 13C; U-100% 15N] Calmodulin, 0.85 mM Cyclic nucleotide-gated cation channel beta-1, 20 mM [U-100% 2H] TRIS, 1 mM Calcium chloride, 100% D2O10%13C_15N_Sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCalmodulin[U-100% 13C; U-100% 15N]1
0.85 mMCyclic nucleotide-gated cation channel beta-1natural abundance1
20 mMTRIS[U-100% 2H]1
1 mMCalcium chloridenatural abundance1
0.5 mMCalmodulin[U-100% 13C; U-100% 15N]2
0.85 mMCyclic nucleotide-gated cation channel beta-1natural abundance2
20 mMTRIS[U-100% 2H]2
1 mMCalcium chloridenatural abundance2
0.5 mMCalmodulin[U-10% 13C; U-100% 15N]3
0.85 mMCyclic nucleotide-gated cation channel beta-1natural abundance3
20 mMTRIS[U-100% 2H]3
1 mMCalcium chloridenatural abundance3
Sample conditionsIonic strength: 1 mM / Label: Condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
HADDOCKBonvinrefinement
HADDOCKBonvinstructure calculation
SparkyGoddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The authors state that for the structure of the calmodulin N-lobe, they used residues 4-81 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 N-lobe, they used residues 4-81 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 the peptide of cyclic-nucleotide-gated olfactory channel (PDB ID - 1SY9, chain B). 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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