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- PDB-6ctb: Apo-Calmodulin Bound to Calcium Voltage Gated Channel 1.2 IQ-Motif -

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Basic information

Entry
Database: PDB / ID: 6ctb
TitleApo-Calmodulin Bound to Calcium Voltage Gated Channel 1.2 IQ-Motif
Components
  • Calmodulin-1
  • Voltage-dependent L-type calcium channel subunit alpha-1C
KeywordsPROTEIN BINDING / calmodulin / surface expression / Cav1.2 / apo-calmodulin / voltage gated channel / calcium / neuronal signaling
Function / homology
Function and homology information


positive regulation of adenylate cyclase activity / regulation of membrane repolarization during action potential / calcium ion transmembrane transport via high voltage-gated calcium channel / high voltage-gated calcium channel activity / cardiac conduction / L-type voltage-gated calcium channel complex / calcium ion transport into cytosol / myosin II complex / voltage-gated calcium channel complex / calcium ion import across plasma membrane ...positive regulation of adenylate cyclase activity / regulation of membrane repolarization during action potential / calcium ion transmembrane transport via high voltage-gated calcium channel / high voltage-gated calcium channel activity / cardiac conduction / L-type voltage-gated calcium channel complex / calcium ion transport into cytosol / myosin II complex / voltage-gated calcium channel complex / calcium ion import across plasma membrane / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / voltage-gated calcium channel activity / T-tubule / postsynaptic density membrane / sarcolemma / calcium ion transmembrane transport / positive regulation of cytosolic calcium ion concentration / perikaryon / calmodulin binding / postsynaptic density / signaling receptor binding / calcium ion binding / dendrite / metal ion binding / membrane / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated ...Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / : / Voltage-dependent channel domain 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 / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-1 / Voltage-dependent L-type calcium channel subunit alpha-1C
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Oryctolagus cuniculus (rabbit)
MethodSOLUTION NMR / simulated annealing
AuthorsTurner, M.L. / Anderson, D.E. / Ames, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY012347 United States
CitationJournal: To Be Published
Title: apo-Calmodulin Bound to Calcium Voltage Gated Channel 1.2 IQ-Motif
Authors: Turner, M.L. / Anderson, D.E. / Ames, J.B.
History
DepositionMar 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 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 1.3May 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: Voltage-dependent L-type calcium channel subunit alpha-1C


Theoretical massNumber of molelcules
Total (without water)19,7712
Polymers19,7712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1910 Å2
ΔGint-11 kcal/mol
Surface area6280 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 200l
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin-1


Mass: 16650.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: calm1
Production host: pBR322 based IG-lambda expression vector (others)
References: UniProt: P0DP33
#2: Protein/peptide Voltage-dependent L-type calcium channel subunit alpha-1C / Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle / Smooth muscle calcium ...Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle / Smooth muscle calcium channel blocker receptor / CACB-receptor / Voltage-gated calcium channel subunit alpha Cav1.2


Mass: 3120.665 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CACNA1C, CACH2, CACN2, CACNL1A1, CCHL1A1
Production host: pBR322 based IG-lambda expression vector (others)
References: UniProt: P15381

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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
122isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1300 uM [U-99% 15N] apo-Calmodulin, 300 uM Calcium Voltage Gated Channel 1.2, 90% H2O/10% D2Oapo-Calmodulin Bound to Cav1.2 IQ Motif15N_apoCalmodulin90% H2O/10% D2O
solution2300 uM [U-99% 15N] Calcium Voltage Gated Channel 1.2, 300 uM apo-Calmodulin, 90% H2O/10% D2O15N Labeled IQ Motif bound to apoCalmodulin15N IQ Motif90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMapo-Calmodulin[U-99% 15N]1
300 uMCalcium Voltage Gated Channel 1.2natural abundance1
300 uMCalcium Voltage Gated Channel 1.2[U-99% 15N]2
300 uMapo-Calmodulinnatural abundance2
Sample conditionsDetails: 20mM Potassium Phosphate pH 6.0, 100mM KCl, 1mM EDTA-d12
Ionic strength: 100 mM / Label: conditions 1 / pH: 6 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: 600 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardpeak picking
HADDOCKBonvinstructure calculation
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
PALESMarkus Zweckstetter and Ad Baxrefinement
RefinementMethod: simulated annealing / Software ordinal: 2 / Details: used with all structures along with rigid docking
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: l / Conformers calculated total number: 200 / Conformers submitted total number: 4

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