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- PDB-4jq0: Voltage-gated sodium channel 1.5 C-terminal domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4jq0
TitleVoltage-gated sodium channel 1.5 C-terminal domain in complex with FGF12B and Ca2+/calmodulin
Components
  • Calmodulin
  • Fibroblast growth factor 12
  • Sodium channel protein type 5 subunit alpha
KeywordsTRANSPORT PROTEIN / EF hand / ion channel / membrane
Function / homology
Function and homology information


regulation of voltage-gated sodium channel activity / regulation of neuronal action potential / 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 ...regulation of voltage-gated sodium channel activity / regulation of neuronal action potential / 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 / regulation of sodium ion transmembrane transporter activity / 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 / neuromuscular process / 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 / sodium channel regulator activity / neuronal action potential
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 / HBGF/FGF family signature. / Voltage gated sodium channel, alpha subunit / Fibroblast growth factor family ...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 / HBGF/FGF family signature. / Voltage gated sodium channel, alpha subunit / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Voltage-gated cation channel calcium and sodium / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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 Beta / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Fibroblast growth factor 12 / Calmodulin-3 / Sodium channel protein type 5 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.84 Å
AuthorsWang, C. / Chung, B.C. / Yan, H. / Wang, H.G. / Lee, S.Y. / Pitt, G.S.
CitationJournal: Nat Commun / Year: 2014
Title: Structural analyses of Ca(2+)/CaM interaction with NaV channel C-termini reveal mechanisms of calcium-dependent regulation.
Authors: Wang, C. / Chung, B.C. / Yan, H. / Wang, H.G. / Lee, S.Y. / Pitt, G.S.
History
DepositionMar 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Structure summary
Revision 1.3Feb 28, 2024Group: 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_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor 12
C: Calmodulin
D: Sodium channel protein type 5 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2887
Polymers66,1283
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-73 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.200, 115.200, 120.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Fibroblast growth factor 12 / FGF-12 / Fibroblast growth factor homologous factor 1 / FHF-1 / Myocyte-activating factor


Mass: 27444.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF12, FGF12B, FHF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61328
#2: Protein Calmodulin / CaM


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, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#3: 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: 21830.613 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
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 7.5
Details: 20% PEG3350, 0.18 M MgSO4, 0.1 M sodium iodide, and CaCl2, pH 7.5, EVAPORATION, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2012
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.83→46.068 Å / Num. all: 3705 / Num. obs: 3705 / % possible obs: 40.58 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.8-3.87113.2
3.87-3.94118.6
3.94-4.01118.1
4.01-4.09122.3
4.09-4.18122.5
4.18-4.2122.8
4.2-4.39124.8
4.39-4.5126
4.5-4.64128.4
4.64-4.79130.7
4.79-4.96135.6
4.96-5.16137
5.16-5.39141.1
5.39-5.67145.3
5.67-6.03155.8
6.03-6.49171.2
6.49-7.15195
7.15-8.181100
8.18-10.29199.4
10.29-50198.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(AutoMR: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(AutoMR: 1.8_1069)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.84→41.57 Å / SU ML: 0.61 / σ(F): 1.38 / Phase error: 35.4 / Stereochemistry target values: ML
Details: THE DIFFRACTION DATA IS HEAVILY ANISOTROPIC (3.8/5.4/6.0 A). AFTER ANISOTROPIC SCALING, THE MODEL REFINES MUCH BETTER WITH INCLUSION OF HIGH-RESOLUTION REFLECTIONS RATHER THAN CUTTING THE ...Details: THE DIFFRACTION DATA IS HEAVILY ANISOTROPIC (3.8/5.4/6.0 A). AFTER ANISOTROPIC SCALING, THE MODEL REFINES MUCH BETTER WITH INCLUSION OF HIGH-RESOLUTION REFLECTIONS RATHER THAN CUTTING THE DATA TO THE LOW RESOLUTION. (6.0 A). ANISOTROPY ALSO GIVES RISE TO THE LOW DATA COMPLETENESS.
RfactorNum. reflection% reflection
Rfree0.3199 202 5.46 %
Rwork0.2534 --
obs0.2571 3700 40.53 %
all-3700 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.84→41.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 4 0 2959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013013
X-RAY DIFFRACTIONf_angle_d0.9794114
X-RAY DIFFRACTIONf_dihedral_angle_d11.328988
X-RAY DIFFRACTIONf_chiral_restr0.057492
X-RAY DIFFRACTIONf_plane_restr0.003545
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)
11.7815-0.18710.63241.5602-0.8560.9149-0.0119-0.46980.1608-0.08641.16060.64740.4262-0.04111.88880.90150.8652-0.76731.14220.2737-0.4898-82.125449.3693-49.3605
22.68240.88061.93841.06720.91812.7329-0.18530.57870.3978-0.3667-0.05340.463-0.22340.0039-0.06381.31240.7139-0.42311.0310.18961.1368-82.665854.2479-36.903
31.0504-0.27460.61971.0423-1.161.6072-0.6592-0.62110.5290.66450.0874-0.09380.46030.3266-0.81730.82321.3429-0.80571.91160.12110.2734-72.581446.1915-42.5207
41.12920.0885-0.38070.4732-0.07840.20380.1481-0.65870.40630.5836-0.61040.4980.5959-0.3569-0.5251.2693-0.27670.8622.2449-0.35470.6307-69.254221.4254-94.6687
55.3651-2.72251.7761.5496-0.96590.66990.3018-0.8103-0.54540.30570.25520.45990.9801-0.2492-0.16421.2935-0.33840.28362.2940.22991.8511-83.493422.608-89.457
65.6747-5.75633.01116.2537-1.9714.73980.3166-0.1782-0.14740.20580.11280.0742-0.4285-0.1891-0.11021.64950.271-0.09711.93970.64071.8447-83.773631.2611-81.0886
71.0076-0.03260.6671.83160.50330.6787-0.3058-0.56170.2293-0.88050.14820.4923-0.2813-0.39060.17590.378-0.37010.14611.9256-0.0470.7716-67.009430.9645-80.5006
84.87320.2349-4.40133.155-0.22784.5254-0.2994-0.5096-0.62920.11930.37641.6229-0.3036-1.7201-0.10661.76770.0318-0.68290.9542-0.0271.4163-66.744423.7008-61.3248
98.85335.01994.80076.1883-0.73446.1785-0.1220.787-1.1016-0.69440.10050.11561.2786-0.1751-0.07220.85730.22630.32851.52490.29670.9056-73.060229.5012-67.7038
102.69530.3834-2.79334.343-1.85995.74710.0849-0.23-0.724-0.37950.38780.2280.50160.5864-0.04920.96850.5163-0.06082.259-0.34521.5205-62.451717.5082-68.7826
110.13070.04340.6490.01410.21056.5614-0.27080.87430.6456-0.3487-0.0829-0.273-0.77360.17870.38960.6021-0.266-0.53082.1490.34011.7035-47.934158.3729-59.379
120.9650.33021.07492.56210.21281.2033-0.38290.30380.7275-0.0894-0.4936-0.3204-0.1797-0.0896-0.76450.3056-0.2069-0.31391.80320.22730.5885-51.126145.7228-61.8851
130.36120.6362-0.54575.4989-1.40272.0755-0.02640.6399-0.20140.07950.2256-0.13880.21-0.0445-0.00590.74640.7162-0.72251.7208-0.13531.5191-57.835549.5958-55.3423
140.84690.52040.43810.29970.32460.3403-0.5224-0.63551.15841.06860.07980.145-1.32510.2896-0.03071.91810.4130.00611.86970.05691.1848-57.990657.041-48.4484
150.0327-0.0746-0.02040.20460.0210.12920.09630.3215-0.7308-0.85670.17250.42670.33820.0743-0.12961.0212-0.25520.16430.5125-0.35871.5984-66.728727.1125-75.8013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 152 )
4X-RAY DIFFRACTION4chain 'C' and (resid 7 through 20 )
5X-RAY DIFFRACTION5chain 'C' and (resid 21 through 40 )
6X-RAY DIFFRACTION6chain 'C' and (resid 41 through 56 )
7X-RAY DIFFRACTION7chain 'C' and (resid 57 through 99 )
8X-RAY DIFFRACTION8chain 'C' and (resid 100 through 112 )
9X-RAY DIFFRACTION9chain 'C' and (resid 113 through 118 )
10X-RAY DIFFRACTION10chain 'C' and (resid 119 through 148 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1786 through 1807 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1808 through 1837 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1838 through 1862 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1863 through 1895 )
15X-RAY DIFFRACTION15chain 'D' and (resid 1896 through 1927 )

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