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- PDB-2kxw: Structure of the C-domain Fragment of apo Calmodulin Bound to the... -

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Basic information

Entry
Database: PDB / ID: 2kxw
TitleStructure of the C-domain Fragment of apo Calmodulin Bound to the IQ motif of Nav1.2
Components
  • Calmodulin
  • Sodium channel protein type 2 subunit alpha
KeywordsCALCIUM-BINDING PROTEIN/METAL TRANSPORT / Action Potential / Amino Acid Motifs / Animals / Autism / Biomolecular / Brain Chemistry / Calcium-Binding Proteins / Calmodulin / Channel / Glutamine / Humans / Ion Channel Gating / Isoleucine / IQ Motif / Metal Transport / Models / Molecular / NaV1.2 / Neuronal / Peptides / Protein Binding / Protein Structure / Sodium Channels / Tertiary / Tyrosine / Voltage-Dependent / Voltage Gated / CALCIUM-BINDING PROTEIN-METAL TRANSPORT complex
Function / homology
Function and homology information


leucine zipper domain binding / membrane depolarization during action potential / axon initial segment / sodium ion binding / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / corpus callosum development / paranode region of axon / voltage-gated sodium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential ...leucine zipper domain binding / membrane depolarization during action potential / axon initial segment / sodium ion binding / intrinsic apoptotic signaling pathway in response to osmotic stress / nerve development / corpus callosum development / paranode region of axon / voltage-gated sodium channel complex / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dentate gyrus development / node of Ranvier / optic nerve development / voltage-gated sodium channel activity / sodium ion transport / axon development / neuronal action potential / sodium ion transmembrane transport / intercalated disc / enzyme regulator activity / T-tubule / myelination / determination of adult lifespan / cerebral cortex development / memory / presynaptic membrane / nervous system development / cellular response to hypoxia / neuron apoptotic process / calmodulin binding / axon / glutamatergic synapse / calcium ion binding / membrane / plasma membrane
Similarity search - Function
Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site ...Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site / 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. / Ion transport domain / Ion transport protein / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Sodium channel protein type 2 subunit alpha / Calmodulin
Similarity search - Component
Biological speciesParamecium tetraurelia (eukaryote)
Rattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsminimized average, model 1
AuthorsFeldkamp, M.D. / Yu, L. / Shea, M.A.
CitationJournal: Structure / Year: 2011
Title: Structural and Energetic Determinants of Apo Calmodulin Binding to the IQ Motif of the Na(V)1.2 Voltage-Dependent Sodium Channel.
Authors: Feldkamp, M.D. / Yu, L. / Shea, M.A.
History
DepositionMay 13, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Sodium channel protein type 2 subunit alpha


Theoretical massNumber of molelcules
Total (without water)11,7862
Polymers11,7862
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 300structures with the lowest energy
RepresentativeModel #1energy minimized average structure

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Components

#1: Protein Calmodulin / / CaM


Mass: 8416.313 Da / Num. of mol.: 1 / Fragment: C-domain (UNP Residues 77-149)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium tetraurelia (eukaryote) / Gene: CAM, GSPATT00015825001 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 DE3 / References: UniProt: P07463
#2: Protein/peptide Sodium channel protein type 2 subunit alpha / / Sodium channel protein type II subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.2 / ...Sodium channel protein type II subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.2 / Sodium channel protein brain II subunit alpha


Mass: 3370.088 Da / Num. of mol.: 1
Fragment: IQ-motif of the Voltage-dependent Sodium Channel (UNP Residues 1901-1927)
Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P04775

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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-13C HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D HN(CO)CA
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11123D (H)CCH-TOCSY
11212D 1H-1H TOCSY
11312D 1H-1H TOCSY
11412D 1H-1H NOESY
11513D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-100% 13C; U-100% 15N] C-domain of apo Calmodulin, 1.5 mM Voltage-dependent Sodium Channel v 1.2, 95% H2O/5% D2O95% H2O/5% D2O
21.5 mM Voltage-dependent Sodium Channel v 1.2, 1.5 mM [U-100% 13C; U-100% 15N] C-domain of apo Calmodulin, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMC-domain of apo Calmodulin (Residues 76-148)-1[U-100% 13C; U-100% 15N]1
1.5 mMVoltage-dependent Sodium Channel v 1.2-21
1.5 mMVoltage-dependent Sodium Channel v 1.2-32
1.5 mMC-domain of apo Calmodulin (Residues 76-148)-4[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIBrukerAvance II8001
Bruker Avance IIBrukerAvance II5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
SPARKYGoddardchemical shift assignment
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1819 / NOE intraresidue total count: 457 / NOE long range total count: 331 / NOE medium range total count: 300 / NOE sequential total count: 298 / Hydrogen bond constraints total count: 46 / Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 54
NMR representativeSelection criteria: energy minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 21 / Maximum lower distance constraint violation: 0.005 Å / Maximum upper distance constraint violation: 0.016 Å
NMR ensemble rmsDistance rms dev: 0.008 Å / Distance rms dev error: 0.001 Å

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