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- PDB-6mud: Voltage-gated sodium channel NaV1.5 C-terminal domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 6mud
TitleVoltage-gated sodium channel NaV1.5 C-terminal domain in complex with Ca2+/Calmodulin
Components
  • Calmodulin-1
  • Sodium channel protein type 5 subunit alpha
KeywordsCALCIUM BINDING/TRANSPORT PROTEIN / voltage-gated ion channel / transport protein / EF-hand domain / CALCIUM BINDING-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


voltage-gated sodium channel activity involved in AV node cell action potential / voltage-gated sodium channel activity involved in bundle of His cell action potential / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / voltage-gated sodium channel activity involved in SA node cell action potential / bundle of His cell action potential / AV node cell action potential / SA node cell action potential / AV node cell to bundle of His cell communication / membrane depolarization during SA node cell action potential / negative regulation of calcium ion transmembrane transporter activity ...voltage-gated sodium channel activity involved in AV node cell action potential / voltage-gated sodium channel activity involved in bundle of His cell action potential / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / voltage-gated sodium channel activity involved in SA node cell action potential / bundle of His cell action potential / AV node cell action potential / SA node cell action potential / AV node cell to bundle of His cell communication / membrane depolarization during SA node cell action potential / negative regulation of calcium ion transmembrane transporter activity / response to denervation involved in regulation of muscle adaptation / membrane depolarization during atrial cardiac muscle cell action potential / cardiac ventricle development / regulation of atrial cardiac muscle cell membrane repolarization / regulation of ventricular cardiac muscle cell membrane depolarization / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / brainstem development / membrane depolarization during AV node cell action potential / positive regulation of action potential / membrane depolarization during bundle of His cell action potential / atrial cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / cardiac conduction system development / telencephalon development / regulation of sodium ion transmembrane transport / regulation of atrial cardiac muscle cell membrane depolarization / membrane depolarization during cardiac muscle cell action potential / membrane depolarization during action potential / positive regulation of sodium ion transport / ventricular cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / regulation of ventricular cardiac muscle cell membrane repolarization / voltage-gated sodium channel complex / regulation of cardiac muscle cell contraction / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Interaction between L1 and Ankyrins / Calmodulin induced events / Reduction of cytosolic Ca++ levels / ankyrin binding / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / voltage-gated sodium channel activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / sodium ion transport / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / fibroblast growth factor binding / RHO GTPases activate PAKs / calcineurin-mediated signaling / odontogenesis of dentin-containing tooth / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / membrane depolarization / DARPP-32 events / intercalated disc / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / lateral plasma membrane / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / eNOS activation / regulation of calcium-mediated signaling
Similarity search - Function
Voltage gated sodium channel, alpha-5 subunit / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / SCN5A-like, C-terminal IQ motif / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily ...Voltage gated sodium channel, alpha-5 subunit / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / SCN5A-like, C-terminal IQ motif / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / EF-hand / : / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Calmodulin-2 / Sodium channel protein type 5 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsGardill, B.R. / Tung, C.C. / 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 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 5 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2716
Polymers33,1102
Non-polymers1604
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-47 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.579, 84.032, 140.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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, UniProt: P0DP24*PLUS
#2: Protein Sodium channel protein type 5 subunit alpha / HH1 / Sodium channel protein cardiac muscle subunit alpha / Sodium channel protein type V subunit ...HH1 / Sodium channel protein cardiac muscle subunit alpha / Sodium channel protein type V subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.5


Mass: 16257.655 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN5A / Production host: Escherichia coli (E. coli) / References: UniProt: Q14524
#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


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 5-15 % (w/v) PEG 4000, 0.1 M Tris, pH 9.5, 0.1 M MgCl2, and 5 % (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-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 17, 2011 / Details: K-B pair of bimorph mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.69→35 Å / Num. obs: 10476 / % possible obs: 93.9 % / Redundancy: 3.25 % / Rrim(I) all: 0.097 / Net I/σ(I): 9.51
Reflection shellResolution: 2.69→2.85 Å / Redundancy: 2.39 % / Mean I/σ(I) obs: 1.89 / Num. unique obs: 1471 / Rrim(I) all: 0.494 / % possible all: 83.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
XDSNovember 11, 2013data reduction
XDSNovember 11, 2013data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→34.31 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 35.519 / SU ML: 0.334 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.849 / ESU R Free: 0.354
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.269 459 4.4 %RANDOM
Rwork0.212 ---
obs0.2147 10016 93.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 138.14 Å2 / Biso mean: 71.222 Å2 / Biso min: 38.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å2-0 Å20 Å2
2---3.79 Å2-0 Å2
3---6.33 Å2
Refinement stepCycle: final / Resolution: 2.69→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 4 15 2222
Biso mean--61.12 50.62 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0142246
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171990
X-RAY DIFFRACTIONr_angle_refined_deg1.0551.663017
X-RAY DIFFRACTIONr_angle_other_deg0.8131.6414684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88223.478138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.35315423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7581516
X-RAY DIFFRACTIONr_chiral_restr0.0490.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022535
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02397
LS refinement shellResolution: 2.69→2.759 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 10 -
Rwork0.43 601 -
all-611 -
obs--75.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4134-1.01492.00292.2341-0.96142.0475-0.2388-0.14590.29820.15580.0043-0.2223-0.0195-0.09920.23460.1355-0.00710.0030.0081-0.03160.4552-6.932-6.521-37.752
22.7013-2.6209-1.72834.63511.02592.3536-0.0102-0.37990.25430.51140.2829-0.3079-0.05560.0434-0.27270.1982-0.0737-0.03650.2013-0.06050.4069-30.55211.441-24.863
30.44551.26570.0777.7752-3.8724.4793-0.37570.32230.1221-0.98040.31940.1037-0.0260.3950.05630.6273-0.22050.03820.56370.14880.5132-32.82622.42-61.364
44.74632.5132-0.68177.16842.54683.4803-0.25130.25430.0197-0.49690.1744-0.46920.09440.62710.07690.2280.00650.09630.250.07110.4305-30.32316.905-51.248
50.44970.6882-0.41299.3894-0.14941.0706-0.18910.17220.0183-0.29020.1722-0.07730.0435-0.17160.01690.2245-0.0134-0.00070.24170.0250.2925-38.93118.067-50.085
60.04330.36620.4449.6717-0.47847.9802-0.0578-0.00530.0562-0.4013-0.02420.4986-0.7038-0.10970.0820.1710.1054-0.08840.3169-0.02880.4344-46.0728.099-56.039
71.62920.69973.64476.4448-0.2788.707-0.07930.0913-0.00010.01960.20110.4038-0.1960.1659-0.12180.0977-0.08170.05160.2830.0130.3651-45.6538.156-49.658
81.3336-2.02433.89483.9651-5.780611.57920.08070.08390.1023-0.0561-0.1919-0.23070.40260.19230.11120.2249-0.0373-0.03470.1178-0.03020.3789-31.5215.311-25.964
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 64
2X-RAY DIFFRACTION2A65 - 147
3X-RAY DIFFRACTION3B1785 - 1801
4X-RAY DIFFRACTION4B1802 - 1837
5X-RAY DIFFRACTION5B1838 - 1862
6X-RAY DIFFRACTION6B1863 - 1878
7X-RAY DIFFRACTION7B1887 - 1894
8X-RAY DIFFRACTION8B1895 - 1920

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