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- PDB-6n4i: Structural basis of Nav1.7 inhibition by a gating-modifier spider... -

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Basic information

Entry
Database: PDB / ID: 6n4i
TitleStructural basis of Nav1.7 inhibition by a gating-modifier spider toxin
Components
  • Beta/omega-theraphotoxin-Tp2a
  • Nav1.7 VSD2-NavAb channel chimera protein
KeywordsMETAL TRANSPORT / sodium channel / toxin / gating-modifier / voltage-gated
Function / homologycalcium channel regulator activity / sodium channel regulator activity / toxin activity / lipid binding / extracellular region / Chem-6OU / Beta/omega-theraphotoxin-Tp2a
Function and homology information
Biological speciesHomo sapiens (human)
Thrixopelma pruriens (green velvet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.541 Å
AuthorsXu, H. / Koth, C.M. / Payandeh, J.
CitationJournal: Cell / Year: 2019
Title: Structural Basis of Nav1.7 Inhibition by a Gating-Modifier Spider Toxin.
Authors: Hui Xu / Tianbo Li / Alexis Rohou / Christopher P Arthur / Foteini Tzakoniati / Evera Wong / Alberto Estevez / Christine Kugel / Yvonne Franke / Jun Chen / Claudio Ciferri / David H Hackos / ...Authors: Hui Xu / Tianbo Li / Alexis Rohou / Christopher P Arthur / Foteini Tzakoniati / Evera Wong / Alberto Estevez / Christine Kugel / Yvonne Franke / Jun Chen / Claudio Ciferri / David H Hackos / Christopher M Koth / Jian Payandeh /
Abstract: Voltage-gated sodium (Nav) channels are targets of disease mutations, toxins, and therapeutic drugs. Despite recent advances, the structural basis of voltage sensing, electromechanical coupling, and ...Voltage-gated sodium (Nav) channels are targets of disease mutations, toxins, and therapeutic drugs. Despite recent advances, the structural basis of voltage sensing, electromechanical coupling, and toxin modulation remains ill-defined. Protoxin-II (ProTx2) from the Peruvian green velvet tarantula is an inhibitor cystine-knot peptide and selective antagonist of the human Nav1.7 channel. Here, we visualize ProTx2 in complex with voltage-sensor domain II (VSD2) from Nav1.7 using X-ray crystallography and cryoelectron microscopy. Membrane partitioning orients ProTx2 for unfettered access to VSD2, where ProTx2 interrogates distinct features of the Nav1.7 receptor site. ProTx2 positions two basic residues into the extracellular vestibule to antagonize S4 gating-charge movement through an electrostatic mechanism. ProTx2 has trapped activated and deactivated states of VSD2, revealing a remarkable ∼10 Å translation of the S4 helix, providing a structural framework for activation gating in voltage-gated ion channels. Finally, our results deliver key templates to design selective Nav channel antagonists.
History
DepositionNov 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references / Structure summary
Category: citation / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct.title
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nav1.7 VSD2-NavAb channel chimera protein
B: Nav1.7 VSD2-NavAb channel chimera protein
C: Nav1.7 VSD2-NavAb channel chimera protein
D: Nav1.7 VSD2-NavAb channel chimera protein
E: Beta/omega-theraphotoxin-Tp2a
F: Beta/omega-theraphotoxin-Tp2a
G: Beta/omega-theraphotoxin-Tp2a
H: Beta/omega-theraphotoxin-Tp2a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,66124
Polymers149,1738
Non-polymers11,48816
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18970 Å2
ΔGint-173 kcal/mol
Surface area52740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.220, 123.530, 123.990
Angle α, β, γ (deg.)90.00, 124.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nav1.7 VSD2-NavAb channel chimera protein


Mass: 33453.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#2: Protein/peptide
Beta/omega-theraphotoxin-Tp2a / Beta/omega-TRTX-Tp2a / ProTx-II / PT-II / Protoxin-2 / ProTx2


Mass: 3839.687 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thrixopelma pruriens (green velvet) / Production host: synthetic construct (others) / References: UniProt: P83476
#3: Chemical
ChemComp-6OU / [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C39H76NO8P / Comment: phospholipid*YM

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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: 4.71 Å3/Da / Density % sol: 73.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.3-2.6M Ammonium sulfate, 100 mM HEPES, pH 7.0; 30% sucrose for cryo
PH range: 4.6-7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 479752 / % possible obs: 99.3 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Net I/σ(I): 10.43
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.76 / Num. unique obs: 35190 / CC1/2: 0.756 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2747: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EK0

5ek0


Resolution: 3.541→36.892 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.23
RfactorNum. reflection% reflection
Rfree0.2942 1373 4.98 %
Rwork0.2745 --
obs0.2755 27544 81.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.541→36.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8312 0 317 0 8629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058822
X-RAY DIFFRACTIONf_angle_d0.85411969
X-RAY DIFFRACTIONf_dihedral_angle_d16.6495071
X-RAY DIFFRACTIONf_chiral_restr0.0471374
X-RAY DIFFRACTIONf_plane_restr0.0051396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5409-3.66730.3372200.3568322X-RAY DIFFRACTION10
3.6673-3.8140.2972480.31011146X-RAY DIFFRACTION36
3.814-3.98740.30941180.2912317X-RAY DIFFRACTION72
3.9874-4.19740.30721390.28343102X-RAY DIFFRACTION97
4.1974-4.45990.28871660.26273194X-RAY DIFFRACTION100
4.4599-4.80360.29711960.24763192X-RAY DIFFRACTION100
4.8036-5.28570.27481940.24483194X-RAY DIFFRACTION100
5.2857-6.04770.29051430.31213237X-RAY DIFFRACTION100
6.0477-7.60850.31891630.343221X-RAY DIFFRACTION100
7.6085-36.89360.28671860.25063246X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 99.0797 Å / Origin y: 248.6897 Å / Origin z: 216.8423 Å
111213212223313233
T0.1316 Å2-0.027 Å2-0.0514 Å2-0.2093 Å2-0.0129 Å2--0.1567 Å2
L0.7162 °2-0.2847 °2-0.0014 °2-0.7802 °2-0.0588 °2--0.7156 °2
S-0.1976 Å °-0.0779 Å °-0.1558 Å °-0.0204 Å °0.2219 Å °-0.0585 Å °-0.1775 Å °0.1176 Å °0.0079 Å °
Refinement TLS groupSelection details: all

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