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- PDB-6mue: Voltage-gated sodium channel NaV1.4 IQ domain in complex with Ca2... -

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Basic information

Entry
Database: PDB / ID: 6mue
TitleVoltage-gated sodium channel NaV1.4 IQ domain in complex with Ca2+/Calmodulin
Components
  • Calmodulin-1
  • Sodium channel protein type 4 subunit alpha
KeywordsCalcium Binding/Transport protein / voltage-gated ion channel / transport protein / IQ domain / Calcium Binding-Transport protein complex
Function / homology
Function and homology information


regulation of skeletal muscle contraction by action potential / choline transport / membrane depolarization during action potential / voltage-gated monoatomic ion channel activity / voltage-gated sodium channel complex / voltage-gated sodium channel activity / regulation of monoatomic ion transmembrane transport / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...regulation of skeletal muscle contraction by action potential / choline transport / membrane depolarization during action potential / voltage-gated monoatomic ion channel activity / voltage-gated sodium channel complex / voltage-gated sodium channel activity / regulation of monoatomic ion transmembrane transport / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / 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) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / sodium ion transport / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / neuronal action potential / Ion transport by P-type ATPases / monoatomic cation transport / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / sodium ion transmembrane transport / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / potassium ion transport / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants
Similarity search - Function
Voltage gated sodium channel, alpha-4 subunit, mammalian / 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 / IQ motif profile. / IQ motif, EF-hand binding site / Voltage-dependent channel domain superfamily / EF-hand domain pair ...Voltage gated sodium channel, alpha-4 subunit, mammalian / 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 / 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
Calmodulin-1 / Sodium channel protein type 4 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGardill, B.R. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-119404 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Crystal structures of Ca2+-calmodulin bound to NaVC-terminal regions suggest role for EF-hand domain in binding and inactivation.
Authors: Gardill, B.R. / Rivera-Acevedo, R.E. / Tung, C.C. / Van Petegem, F.
History
DepositionOct 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin-1
B: Sodium channel protein type 4 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7426
Polymers20,5822
Non-polymers1604
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-42 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.580, 24.433, 60.720
Angle α, β, γ (deg.)90.000, 112.630, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Calmodulin-1 /


Mass: 17047.744 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 Sodium channel protein type 4 subunit alpha / / Mu-1 / SkM1 / Sodium channel protein skeletal muscle subunit alpha / Sodium channel protein type IV ...Mu-1 / SkM1 / Sodium channel protein skeletal muscle subunit alpha / Sodium channel protein type IV subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.4


Mass: 3534.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P15390
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0 and 55 % (v/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 14964 / % possible obs: 98.3 % / Redundancy: 3.81 % / Rrim(I) all: 0.093 / Net I/σ(I): 9.66
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.37 % / Mean I/σ(I) obs: 1.68 / Num. unique obs: 2235 / Rrim(I) all: 0.744 / % possible all: 91.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
XDSOctober 15, 2015data reduction
XDSOctober 15, 2015data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4djc

4djc


Resolution: 1.9→33.07 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.865 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.165
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 647 5 %RANDOM
Rwork0.2136 ---
obs0.2159 12292 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.23 Å2 / Biso mean: 36.906 Å2 / Biso min: 19.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å20.77 Å2
2---1.19 Å20 Å2
3----0.91 Å2
Refinement stepCycle: final / Resolution: 1.9→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 4 45 1253
Biso mean--30.49 38.51 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0141286
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171116
X-RAY DIFFRACTIONr_angle_refined_deg1.241.6641738
X-RAY DIFFRACTIONr_angle_other_deg0.9721.6512624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5645166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26923.67179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94215234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.256159
X-RAY DIFFRACTIONr_chiral_restr0.0670.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021506
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02230
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 46 -
Rwork0.329 879 -
all-925 -
obs--99.89 %

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