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- PDB-4ovn: Voltage-gated Sodium Channel 1.5 (Nav1.5) C-terminal domain in co... -

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Basic information

Entry
Database: PDB / ID: 4ovn
TitleVoltage-gated Sodium Channel 1.5 (Nav1.5) C-terminal domain in complex with Calmodulin poised for activation
Components
  • Calmodulin
  • Sodium channel protein type 5 subunit alpha
KeywordsMETAL BINDING PROTEIN / SCN5A / Voltage Gated Sodium Channel / Calmodulin
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 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 / response to denervation involved in regulation of muscle adaptation / cardiac ventricle development ...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 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 / response to denervation involved in regulation of muscle adaptation / cardiac ventricle development / regulation of ventricular cardiac muscle cell membrane depolarization / membrane depolarization during atrial cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane repolarization / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / regulation of sodium ion transmembrane transport / brainstem development / membrane depolarization during AV node cell action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / membrane depolarization during bundle of His cell action potential / positive regulation of action potential / atrial cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / telencephalon development / cardiac conduction system development / regulation of atrial cardiac muscle cell membrane depolarization / : / establishment of protein localization to mitochondrial membrane / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / type 3 metabotropic glutamate receptor binding / ventricular cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / regulation of ventricular cardiac muscle cell membrane repolarization / regulation of cardiac muscle cell contraction / voltage-gated sodium channel complex / membrane depolarization during action potential / Interaction between L1 and Ankyrins / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / regulation of synaptic vesicle endocytosis / 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 / voltage-gated sodium channel activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ankyrin binding / 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 / regulation of synaptic vesicle exocytosis / sodium ion transport / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / Activation of RAC1 downstream of NMDARs / response to corticosterone / nitric-oxide synthase binding / positive regulation of ryanodine-sensitive calcium-release channel activity / fibroblast growth factor binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / protein phosphatase activator activity / regulation of heart rate by cardiac conduction / odontogenesis of dentin-containing tooth / RHO GTPases activate PAKs / membrane depolarization / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / adenylate cyclase binding / catalytic complex / intercalated disc / DARPP-32 events / detection of calcium ion / sodium ion transmembrane transport / lateral plasma membrane / regulation of cardiac muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / neuronal action potential / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / cellular response to interferon-beta / positive regulation of DNA binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion
Similarity search - Function
iswi atpase / Voltage gated sodium channel, alpha-5 subunit / 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 / Voltage-dependent channel domain superfamily ...iswi atpase / Voltage gated sodium channel, alpha-5 subunit / 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 / Voltage-dependent channel domain superfamily / EF-hand / Recoverin; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Calmodulin-1 / Calmodulin-3 / Sodium channel protein type 5 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsGabelli, S.B. / Bianchet, M.A. / Boto, A. / Jakoncic, J. / Tomaselli, G.F. / Amzel, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)RO1 HL050411-15A1 United States
CitationJournal: Nat Commun / Year: 2014
Title: Regulation of the NaV1.5 cytoplasmic domain by calmodulin.
Authors: Gabelli, S.B. / Boto, A. / Kuhns, V.H. / Bianchet, M.A. / Farinelli, F. / Aripirala, S. / Yoder, J. / Jakoncic, J. / Tomaselli, G.F. / Amzel, L.M.
History
DepositionDec 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Derived calculations
Revision 1.2Apr 8, 2015Group: Derived calculations
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.country ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
F: Sodium channel protein type 5 subunit alpha
B: Calmodulin
G: Sodium channel protein type 5 subunit alpha
C: Calmodulin
H: Sodium channel protein type 5 subunit alpha
D: Calmodulin
I: Sodium channel protein type 5 subunit alpha
E: Calmodulin
J: Sodium channel protein type 5 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,93035
Polymers179,82210
Non-polymers1,10825
Water1,11762
1
A: Calmodulin
F: Sodium channel protein type 5 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2548
Polymers35,9642
Non-polymers2896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-17 kcal/mol
Surface area17330 Å2
MethodPISA
2
B: Calmodulin
G: Sodium channel protein type 5 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2287
Polymers35,9642
Non-polymers2645
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-18 kcal/mol
Surface area16810 Å2
MethodPISA
3
C: Calmodulin
H: Sodium channel protein type 5 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2779
Polymers35,9642
Non-polymers3137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-16 kcal/mol
Surface area17340 Å2
MethodPISA
4
D: Calmodulin
I: Sodium channel protein type 5 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0626
Polymers35,9642
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-20 kcal/mol
Surface area17050 Å2
MethodPISA
5
E: Calmodulin
J: Sodium channel protein type 5 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1095
Polymers35,9642
Non-polymers1453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-17 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.128, 99.006, 109.281
Angle α, β, γ (deg.)90.000, 106.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 10 molecules ABCDEFGHIJ

#1: Protein
Calmodulin / CaM


Mass: 17321.496 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP23*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: 18642.982 Da / Num. of mol.: 5 / Fragment: C-terminal Domain (UNP residue 1773-1929)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCN5A / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14524

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Non-polymers , 4 types, 87 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 15% PEG 4K, 0.2 M MgSO4 and 10% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.798→28.9 Å / Num. obs: 48516 / % possible obs: 90.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 77.01 Å2 / Rmerge(I) obs: 0.116 / Χ2: 78.182 / Net I/av σ(I): 32.384 / Net I/σ(I): 11.5 / Num. measured all: 311500
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.745 / Num. unique all: 2626 / Χ2: 0.089 / Rejects: 0 / % possible all: 58.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→28.7 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 0.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.282 4588 4.94 %RANDOM
Rwork0.211 92851 --
obs0.215 92851 88.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 243.42 Å2 / Biso mean: 93.06 Å2 / Biso min: 29.91 Å2
Refinement stepCycle: final / Resolution: 2.8→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11669 0 53 62 11784
Biso mean--99.71 74.28 -
Num. residues----1458
LS refinement shellResolution: 2.8→2.83 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.4318 91 -
Rwork0.367 1694 -
all-1785 -
obs--52 %
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)
11.2472-0.1763-0.34571.15190.22331.25440.0199-0.05360.3706-0.14410.0583-0.29790.04570.28340.00010.61990.02410.02420.79180.02270.849496.002720.039114.9656
20.5639-0.4476-0.63871.69780.8351.24040.0778-0.09810.53840.12820.1511-0.2335-0.08560.277-00.6254-0.0447-0.0360.7156-0.09480.99687.273135.13126.2727
31.31690.1627-0.1912.45770.78050.2897-0.17180.4368-0.0324-0.46770.3175-0.3596-0.06840.0466-00.9796-0.10640.17720.8584-0.08450.895560.692450.68924.7351
41.28590.23760.1841.21550.46990.57940.09370.29080.1375-0.3480.1304-0.1982-0.0939-0.008-00.8268-0.056-0.03010.7484-0.06050.620943.854938.532923.8563
51.4464-0.3555-0.70681.6366-0.65441.6185-0.2538-0.08460.02540.11480.2349-0.21330.15120.175-0.00010.7894-0.0183-0.00070.79-0.06740.735112.142347.07276.5033
60.9905-0.5253-0.20551.6722-0.62650.6848-0.10710.25910.3587-0.22320.21750.00720.1116-0.1132-0.00010.7398-0.118-0.04510.85180.01010.5421-7.851949.518171.5899
70.8448-0.46970.43630.9999-0.56021.4633-0.1040.0792-0.1456-0.34890.10690.09530.4328-0.027300.8119-0.0615-0.0150.7112-0.00840.785232.519615.018243.4544
80.7525-0.17040.55090.6649-0.54042.4367-0.1072-0.10440.10540.1740.10820.22690.09360.1841-00.61730.0432-0.04450.614-0.02550.689528.443422.645562.4738
92.13430.92150.13011.7072-0.61081.1196-0.22870.85390.2898-0.43640.0820.15970.29370.184900.8378-0.01660.01931.09310.21160.8827100.440930.0996-35.7531
101.37191.0955-0.66131.002-0.53751.1741-0.09310.2825-0.0262-0.05280.10540.17380.25630.0254-0.00010.6952-0.004-0.06280.70880.020.624493.925518.5753-18.9198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 148
2X-RAY DIFFRACTION2F1782 - 1927
3X-RAY DIFFRACTION3B5 - 148
4X-RAY DIFFRACTION4G1783 - 1926
5X-RAY DIFFRACTION5C4 - 148
6X-RAY DIFFRACTION6H1778 - 1927
7X-RAY DIFFRACTION7D4 - 148
8X-RAY DIFFRACTION8I1784 - 1926
9X-RAY DIFFRACTION9E5 - 148
10X-RAY DIFFRACTION10J1776 - 1926

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