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- PDB-5ek0: Human Nav1.7-VSD4-NavAb in complex with GX-936. -

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Basic information

Entry
Database: PDB / ID: 5ek0
TitleHuman Nav1.7-VSD4-NavAb in complex with GX-936.
ComponentsChimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha
KeywordsMETAL TRANSPORT / membrane protein / ion channel / voltage-gated sodium channel / small molecule antagonist
Function / homology
Function and homology information


detection of mechanical stimulus involved in sensory perception / voltage-gated sodium channel complex / high voltage-gated calcium channel activity / voltage-gated sodium channel activity / Interaction between L1 and Ankyrins / sodium ion transport / voltage-gated calcium channel complex / behavioral response to pain / Phase 0 - rapid depolarisation / calcium ion import across plasma membrane ...detection of mechanical stimulus involved in sensory perception / voltage-gated sodium channel complex / high voltage-gated calcium channel activity / voltage-gated sodium channel activity / Interaction between L1 and Ankyrins / sodium ion transport / voltage-gated calcium channel complex / behavioral response to pain / Phase 0 - rapid depolarisation / calcium ion import across plasma membrane / detection of temperature stimulus involved in sensory perception of pain / sodium ion transmembrane transport / monoatomic cation channel activity / sensory perception of pain / post-embryonic development / Sensory perception of sweet, bitter, and umami (glutamate) taste / response to toxic substance / circadian rhythm / inflammatory response / axon / identical protein binding / plasma membrane
Similarity search - Function
Voltage-gated potassium channels. Chain C / 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 / Helix Hairpins - #70 / Short calmodulin-binding motif containing conserved Ile and Gln residues. ...Voltage-gated potassium channels. Chain C / 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 / Helix Hairpins - #70 / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-5P2 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein / Sodium channel protein type 9 subunit alpha
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 Å
AuthorsAhuja, S. / Mukund, S. / Starovasnik, M.A. / Koth, C.M. / Payandeh, J.
CitationJournal: Science / Year: 2015
Title: Structural basis of Nav1.7 inhibition by an isoform-selective small-molecule antagonist.
Authors: Ahuja, S. / Mukund, S. / Deng, L. / Khakh, K. / Chang, E. / Ho, H. / Shriver, S. / Young, C. / Lin, S. / Johnson, J.P. / Wu, P. / Li, J. / Coons, M. / Tam, C. / Brillantes, B. / Sampang, H. ...Authors: Ahuja, S. / Mukund, S. / Deng, L. / Khakh, K. / Chang, E. / Ho, H. / Shriver, S. / Young, C. / Lin, S. / Johnson, J.P. / Wu, P. / Li, J. / Coons, M. / Tam, C. / Brillantes, B. / Sampang, H. / Mortara, K. / Bowman, K.K. / Clark, K.R. / Estevez, A. / Xie, Z. / Verschoof, H. / Grimwood, M. / Dehnhardt, C. / Andrez, J.C. / Focken, T. / Sutherlin, D.P. / Safina, B.S. / Starovasnik, M.A. / Ortwine, D.F. / Franke, Y. / Cohen, C.J. / Hackos, D.H. / Koth, C.M. / Payandeh, J.
History
DepositionNov 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha
B: Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha
C: Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha
D: Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,03229
Polymers138,4724
Non-polymers16,56025
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27610 Å2
ΔGint-231 kcal/mol
Surface area48390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.420, 188.830, 171.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha / euroendocrine sodium channel / hNE-Na / Peripheral sodium channel 1 / PN1 / Sodium channel protein ...euroendocrine sodium channel / hNE-Na / Peripheral sodium channel 1 / PN1 / Sodium channel protein type IX subunit alpha / Voltage-gated sodium channel subunit alpha Nav1.7


Mass: 34618.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri, Homo sapiens / Strain: RM4018 / Gene: Abu_1752, SCN9A, NENA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5, UniProt: Q15858
#2: Chemical...
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#3: Chemical
ChemComp-5P2 / 3-cyano-4-[2-[2-(1-ethylazetidin-3-yl)pyrazol-3-yl]-4-(trifluoromethyl)phenoxy]-~{N}-(1,2,4-thiadiazol-5-yl)benzenesulfonamide / GX-936


Mass: 575.586 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H20F3N7O3S2
Sequence detailsThis construct is a chimera between the bacterial NavAb channel (A8EVM5) and human Nav1.7 (Q1585-3).

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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: 4.94 Å3/Da / Density % sol: 75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.4 / Details: 2.2 ammonium sulfate, 100 mM sodium citrate pH 5.4

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: data from 2 single crystals merged
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.53→26.59 Å / Num. obs: 33851 / % possible obs: 99.6 % / Redundancy: 9 % / Biso Wilson estimate: 96.72 Å2 / Rmerge(I) obs: 0.149 / Net I/σ(I): 10.4
Reflection shellResolution: 3.53→3.95 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
Aimlessdata scaling
PHENIXphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVY

3rvy


Resolution: 3.53→26.59 Å / Cor.coef. Fo:Fc: 0.8358 / Cor.coef. Fo:Fc free: 0.8205 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.842 / SU Rfree Blow DPI: 0.466
RfactorNum. reflection% reflectionSelection details
Rfree0.2719 1714 5.06 %RANDOM
Rwork0.2427 ---
obs0.2442 33851 99.73 %-
Displacement parametersBiso mean: 106.05 Å2
Baniso -1Baniso -2Baniso -3
1--42.2998 Å20 Å20 Å2
2--47.9394 Å20 Å2
3----5.6396 Å2
Refine analyzeLuzzati coordinate error obs: 0.871 Å
Refinement stepCycle: 1 / Resolution: 3.53→26.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8082 0 489 0 8571
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018780HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.111913HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3036SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes120HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1211HARMONIC5
X-RAY DIFFRACTIONt_it8780HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion22.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1150SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11147SEMIHARMONIC4
LS refinement shellResolution: 3.53→3.64 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2588 148 5.2 %
Rwork0.2473 2697 -
all0.2479 2845 -
obs--99.73 %

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