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- PDB-4djc: 1.35 A crystal structure of the NaV1.5 DIII-IV-Ca/CaM complex -

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Basic information

Entry
Database: PDB / ID: 4djc
Title1.35 A crystal structure of the NaV1.5 DIII-IV-Ca/CaM complex
Components
  • Calmodulin
  • Sodium channel protein type 5 subunit alpha
Keywordscalcium-binding protein / EF-Hand
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 / response to denervation involved in regulation of muscle adaptation ...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 / 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 / : / : / 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 / establishment of protein localization to mitochondrial membrane / membrane depolarization during action potential / positive regulation of sodium ion transport / type 3 metabotropic glutamate receptor binding / negative regulation of peptidyl-threonine phosphorylation / 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 / Activation of Ca-permeable Kainate Receptor / ankyrin binding / 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 / positive regulation of DNA binding / 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 / nitric-oxide synthase binding / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / 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 / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / calcineurin-mediated signaling / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / fibroblast growth factor binding / odontogenesis of dentin-containing tooth / regulation of synaptic vesicle endocytosis / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / positive regulation of protein autophosphorylation / Long-term potentiation / protein phosphatase activator activity / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / membrane depolarization / intercalated disc / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity
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 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
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Calmodulin-1 / Calmodulin-3 / Sodium channel protein type 5 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSarhan, M.F. / Tung, C.-C. / Van Petegem, F. / Ahern, C.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystallographic basis for calcium regulation of sodium channels.
Authors: Sarhan, M.F. / Tung, C.C. / Van Petegem, F. / Ahern, C.A.
History
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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_alt_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_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr1_label_alt_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.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: Calmodulin
B: Sodium channel protein type 5 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,94815
Polymers21,2472
Non-polymers70113
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-13 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.380, 72.720, 97.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Calmodulin / CaM


Mass: 17124.805 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
#2: Protein/peptide 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: 4121.912 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: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 60% Isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9749 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 8, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9749 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 45088 / Num. obs: 44657 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.35→1.38 Å / % possible all: 92.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→29.55 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.787 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17626 2234 5 %RANDOM
Rwork0.15274 ---
obs0.15391 42422 100 %-
all-44657 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.786 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å20 Å2
2--2.25 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 40 161 1457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221402
X-RAY DIFFRACTIONr_bond_other_d0.0010.02923
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9791901
X-RAY DIFFRACTIONr_angle_other_deg1.09732288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5325193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03926.80672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3315261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.713155
X-RAY DIFFRACTIONr_chiral_restr0.1110.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021597
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02256
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.961.5863
X-RAY DIFFRACTIONr_mcbond_other1.2711.5353
X-RAY DIFFRACTIONr_mcangle_it2.92521392
X-RAY DIFFRACTIONr_scbond_it4.2443539
X-RAY DIFFRACTIONr_scangle_it6.284.5495
X-RAY DIFFRACTIONr_rigid_bond_restr1.99732325
X-RAY DIFFRACTIONr_sphericity_free10.293165
X-RAY DIFFRACTIONr_sphericity_bonded7.62132305
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 150 -
Rwork0.266 2834 -
obs--99.97 %

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