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- PDB-4dck: Crystal structure of the C-terminus of voltage-gated sodium chann... -

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Basic information

Entry
Database: PDB / ID: 4dck
TitleCrystal structure of the C-terminus of voltage-gated sodium channel in complex with FGF13 and CaM
Components
  • Calmodulin
  • Fibroblast growth factor 13
  • Sodium channel protein type 5 subunit alpha
KeywordsTRANSPORT PROTEIN/SIGNALING PROTEIN / IQ-motif / EF-hand / Voltage-gated Sodium Channel regulation / Nav1.5 CTD binds to FGF13 and CaM. CaM binds to Ca2+. / TRANSPORT PROTEIN-TRANSPORT PROTEIN REGULATOR-SIGNALING PROTEIN complex / TRANSPORT PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


establishment of neuroblast polarity / 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 / regulation of cardiac muscle cell action potential involved in regulation of contraction / AV node cell action potential / SA node cell action potential / AV node cell to bundle of His cell communication ...establishment of neuroblast polarity / 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 / regulation of cardiac muscle cell action potential involved in regulation of contraction / 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 / positive regulation of voltage-gated sodium channel activity / negative regulation of collateral sprouting / 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 / branching morphogenesis of a nerve / 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 / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / 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 / establishment of protein localization to mitochondrial membrane / positive regulation of sodium ion transport / negative regulation of microtubule depolymerization / negative regulation of peptidyl-threonine phosphorylation / 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 / voltage-gated sodium channel complex / inhibitory synapse assembly / 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 / positive regulation of DNA binding / PKA activation / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / positive regulation of peptidyl-threonine phosphorylation / 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 / regulation of synaptic vesicle exocytosis / 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 / beta-tubulin binding / 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 / cerebral cortex cell migration / microtubule polymerization / regulation of heart rate by cardiac conduction / regulation of synaptic vesicle endocytosis / Ion transport by P-type ATPases / positive regulation of protein autophosphorylation / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity
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 / HBGF/FGF family signature. / SCN5A-like, C-terminal IQ motif / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / 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 / HBGF/FGF family signature. / SCN5A-like, C-terminal IQ motif / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Cytokine IL1/FGF / 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 / Calmodulin-3 / Sodium channel protein type 5 subunit alpha / Fibroblast growth factor 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChung, B.C. / Wang, C. / Yan, H. / Pitt, G.S. / Lee, S.Y.
CitationJournal: Structure / Year: 2012
Title: Crystal Structure of the Ternary Complex of a NaV C-Terminal Domain, a Fibroblast Growth Factor Homologous Factor, and Calmodulin.
Authors: Wang, C. / Chung, B.C. / Yan, H. / Lee, S.Y. / Pitt, G.S.
History
DepositionJan 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Feb 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.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_asym_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

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Assembly

Deposited unit
A: Sodium channel protein type 5 subunit alpha
B: Calmodulin
C: Fibroblast growth factor 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9056
Polymers57,8323
Non-polymers733
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-43 kcal/mol
Surface area22480 Å2
MethodPISA
2
A: Sodium channel protein type 5 subunit alpha
B: Calmodulin
C: Fibroblast growth factor 13
hetero molecules

A: Sodium channel protein type 5 subunit alpha
B: Calmodulin
C: Fibroblast growth factor 13
hetero molecules

A: Sodium channel protein type 5 subunit alpha
B: Calmodulin
C: Fibroblast growth factor 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,71518
Polymers173,4969
Non-polymers2199
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area20840 Å2
ΔGint-178 kcal/mol
Surface area60420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.041, 126.041, 126.041
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-362-

HOH

DetailsThe C-terminus of voltage-gated sodium channel is a monomer and in complex with FGF13 and CaM. So it is heterotrimer (ternary complex).

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Components

#1: 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: 19369.891 Da / Num. of mol.: 1 / Fragment: C-terminal domain of Nav1.5
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
#2: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 1 / Fragment: Calmodulin
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 Fibroblast growth factor 13 / FGF-13 / Fibroblast growth factor homologous factor 2 / FHF-2


Mass: 21609.592 Da / Num. of mol.: 1 / Fragment: FGF13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF13, FHF2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92913
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG400, 150mM Magnesium Acetate, 50mM Sodium Cacodylate , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11
SYNCHROTRONAPS 24-ID-C21
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDAug 1, 2011
ADSC QUANTUM 3152CCDAug 22, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal, Si 111SINGLE WAVELENGTHMx-ray1
2double crystal, Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 33622 / Num. obs: 33622 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 39.3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.21-2.251,294.8
2.25-2.291,297
2.29-2.341,298.5
2.34-2.41,298.5
2.4-2.461,298.9
2.46-2.531,298.5
2.53-2.61,299
2.6-2.681,299.4
2.68-2.781,299.4
2.78-2.891,299.5
2.89-3.021,299.6
3.02-3.181,299.8
3.18-3.381,299.8
3.38-3.641,299.9
3.64-4.011,299.9
4.01-4.591,299.9
4.59-5.781,2100
5.78-501,299.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.reflection_file_editor: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.1_743phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→39.858 Å / SU ML: 0.48 / σ(F): 1.44 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1701 5 %Random
Rwork0.2098 ---
obs0.2107 -99.76 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.578 Å2 / ksol: 0.334 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 3 202 3693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113563
X-RAY DIFFRACTIONf_angle_d0.8234798
X-RAY DIFFRACTIONf_dihedral_angle_d14.4861343
X-RAY DIFFRACTIONf_chiral_restr0.056521
X-RAY DIFFRACTIONf_plane_restr0.004622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.26480.26381400.26252641X-RAY DIFFRACTION99
2.2648-2.33790.28441410.24552656X-RAY DIFFRACTION100
2.3379-2.42150.25181400.23492657X-RAY DIFFRACTION100
2.4215-2.51840.25581400.23222693X-RAY DIFFRACTION100
2.5184-2.6330.31091440.2412665X-RAY DIFFRACTION100
2.633-2.77180.26361380.23912673X-RAY DIFFRACTION100
2.7718-2.94540.2411430.23562679X-RAY DIFFRACTION100
2.9454-3.17270.24511390.23522692X-RAY DIFFRACTION100
3.1727-3.49190.2521430.21662701X-RAY DIFFRACTION100
3.4919-3.99670.20661430.19862705X-RAY DIFFRACTION100
3.9967-5.03390.18021400.17242746X-RAY DIFFRACTION100
5.0339-39.86420.21761500.19952818X-RAY DIFFRACTION100

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