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- EMDB-0342: CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with... -
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Basic information
Entry | Database: EMDB / ID: EMD-0342 | |||||||||
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Title | CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2 | |||||||||
![]() | Map generated with a mask including Nav (with truncated C-terminal coiled-coil), ProTx2 and Fv fragment. | |||||||||
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Function / homology | ![]() detection of mechanical stimulus involved in sensory perception / membrane depolarization during action potential / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / Phase 0 - rapid depolarisation / behavioral response to pain / detection of temperature stimulus involved in sensory perception of pain ...detection of mechanical stimulus involved in sensory perception / membrane depolarization during action potential / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / Phase 0 - rapid depolarisation / behavioral response to pain / detection of temperature stimulus involved in sensory perception of pain / calcium channel regulator activity / sodium ion transmembrane transport / sodium channel regulator activity / sensory perception of pain / post-embryonic development / circadian rhythm / response to toxic substance / Sensory perception of sweet, bitter, and umami (glutamate) taste / toxin activity / inflammatory response / axon / lipid binding / extracellular region / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | Xu H / Rohou A / Arthur CP / Estevez A / Ciferri C / Payandeh J / Koth CM | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 164.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 26.4 KB 26.4 KB | Display Display | ![]() |
Images | ![]() | 106.8 KB | ||
Others | ![]() ![]() ![]() | 164.8 MB 32.6 MB 32.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 532.6 KB | Display | ![]() |
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Full document | ![]() | 532.2 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 17.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6n4rMC ![]() 0341C ![]() 6n4iC ![]() 6n4qC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Map generated with a mask including Nav (with truncated C-terminal coiled-coil), ProTx2 and Fv fragment. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map for the main map.
File | emd_0342_additional.map | ||||||||||||
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Annotation | Unsharpened map for the main map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM half map 2
File | emd_0342_half_map_1.map | ||||||||||||
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Annotation | EM half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM half map 1
File | emd_0342_half_map_2.map | ||||||||||||
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Annotation | EM half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Nav1.7 VSD2 in complex with ProTx2 and an anti-Nav Fab
Entire | Name: Nav1.7 VSD2 in complex with ProTx2 and an anti-Nav Fab |
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Components |
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-Supramolecule #1: Nav1.7 VSD2 in complex with ProTx2 and an anti-Nav Fab
Supramolecule | Name: Nav1.7 VSD2 in complex with ProTx2 and an anti-Nav Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 245 KDa |
-Macromolecule #1: Nav1.7 VSD2-NavAb chimera
Macromolecule | Name: Nav1.7 VSD2-NavAb chimera / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.453512 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MDYKDDDDKG SLVPRGSHMY LRITNIVESS FFTKFIIYLI VLNTLFMAME HHPMTEEFKN VLAIGNLVFT GIFAIEIILR IYVHRISFF KDPWSLFDSL IVTLSLVELF LADVEGLSVL RSFRLLRVFR LVTAVPQMRK IVSALISVIP GMLSVIALMT L FFYIFAIM ...String: MDYKDDDDKG SLVPRGSHMY LRITNIVESS FFTKFIIYLI VLNTLFMAME HHPMTEEFKN VLAIGNLVFT GIFAIEIILR IYVHRISFF KDPWSLFDSL IVTLSLVELF LADVEGLSVL RSFRLLRVFR LVTAVPQMRK IVSALISVIP GMLSVIALMT L FFYIFAIM ATQLFGERFP EWFGTLGESF YTLFQVMTLE SWSMGIVRPL MEVYPYAWVF FIPFIFVVTF VMINLVVAIC VD AMAILNQ KEEQHIIDEV QSHEDNINNE IIKLREEIVE LKELIKTSLK N |
-Macromolecule #2: Beta/omega-theraphotoxin-Tp2a
Macromolecule | Name: Beta/omega-theraphotoxin-Tp2a / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 3.839687 KDa |
Sequence | String: YCQKWMWTCD SERKCCEGMV CRLWCKKKLW |
-Macromolecule #3: Fab light chain
Macromolecule | Name: Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.48391 KDa |
Sequence | String: EIVLTQSPAL MAASPGEKVT ITCSVSLSIS SSNLFWYQQK SETSPKPWIY GTSKLASGVP VRFSGSGSGT SYSLTISSME AEDAATYYC QQWSSHSFTF GGGTKLEIKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD ...String: EIVLTQSPAL MAASPGEKVT ITCSVSLSIS SSNLFWYQQK SETSPKPWIY GTSKLASGVP VRFSGSGSGT SYSLTISSME AEDAATYYC QQWSSHSFTF GGGTKLEIKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD SKDSTYSMSS TLTLTKDEYE RHNSYTCEAT HKTSTSPIVK SFNRNEC |
-Macromolecule #4: Fab heavy chain
Macromolecule | Name: Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.523518 KDa |
Sequence | String: EVQLVESGGG LVKPGGSLKL SCAASGFTFS NYAMSWVRQT PEKRLEWVAT ISNGGRYTYY PDSVKGRFTI SRDNAKNSLY LQMSSLRSE DTAMYYCARH LYRYDVGGAL DYWGQGTSVT VSSAKTTAPS VYPLAPVCGD TTGSSVTLGC LVKGYFPEPV T LTWNSGSL ...String: EVQLVESGGG LVKPGGSLKL SCAASGFTFS NYAMSWVRQT PEKRLEWVAT ISNGGRYTYY PDSVKGRFTI SRDNAKNSLY LQMSSLRSE DTAMYYCARH LYRYDVGGAL DYWGQGTSVT VSSAKTTAPS VYPLAPVCGD TTGSSVTLGC LVKGYFPEPV T LTWNSGSL SSGVHTFPAV LQSDLYTLSS SVTVTSSTWP SQSITCNVAH PASSTKVDKK IEPRGPTIKP |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 Details: 10 mM Tris pH 8.0, 100 mM NaCl, 0.06% FA3, 0.1 mg/ml POPC:POPE:POPG mixed at molar ratio 3:1:1 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Grid was coated with a thin layer of gold |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Apply 3 uL, blot 2.5s. Ted Pella 595 filter paper.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 25084 / Average exposure time: 10.0 sec. / Average electron dose: 41.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |