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Yorodumi- EMDB-22661: Structure of NavAb/Nav1.7-VS2A chimera trapped in the resting sta... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22661 | |||||||||||||||
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Title | Structure of NavAb/Nav1.7-VS2A chimera trapped in the resting state by tarantula toxin m3-Huwentoxin-IV | |||||||||||||||
Map data | EM map without post-cut-off B-factor sharpening | |||||||||||||||
Sample |
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Function / homology | Function and homology information detection of mechanical stimulus involved in sensory perception / host cell presynaptic membrane / 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 / ion channel inhibitor activity / detection of maltose stimulus / sodium ion transport ...detection of mechanical stimulus involved in sensory perception / host cell presynaptic membrane / 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 / ion channel inhibitor activity / detection of maltose stimulus / sodium ion transport / maltose transport complex / Phase 0 - rapid depolarisation / behavioral response to pain / carbohydrate transport / detection of temperature stimulus involved in sensory perception of pain / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / sodium ion transmembrane transport / sodium channel regulator activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / sensory perception of pain / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / post-embryonic development / circadian rhythm / response to toxic substance / Sensory perception of sweet, bitter, and umami (glutamate) taste / outer membrane-bounded periplasmic space / toxin activity / periplasmic space / inflammatory response / axon / DNA damage response / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Escherichia coli (E. coli) / Haplopelma schmidti (Chinese earth tiger) / Arcobacter butzleri (strain RM4018) (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
Authors | Wisedchaisri G / Tonggu L / Gamal El-Din TM / McCord E / Zheng N / Catterall WA | |||||||||||||||
Funding support | United States, 4 items
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Citation | Journal: Mol Cell / Year: 2021 Title: Structural Basis for High-Affinity Trapping of the Na1.7 Channel in Its Resting State by Tarantula Toxin. Authors: Goragot Wisedchaisri / Lige Tonggu / Tamer M Gamal El-Din / Eedann McCord / Ning Zheng / William A Catterall / Abstract: Voltage-gated sodium channels initiate electrical signals and are frequently targeted by deadly gating-modifier neurotoxins, including tarantula toxins, which trap the voltage sensor in its resting ...Voltage-gated sodium channels initiate electrical signals and are frequently targeted by deadly gating-modifier neurotoxins, including tarantula toxins, which trap the voltage sensor in its resting state. The structural basis for tarantula-toxin action remains elusive because of the difficulty of capturing the functionally relevant form of the toxin-channel complex. Here, we engineered the model sodium channel NaAb with voltage-shifting mutations and the toxin-binding site of human Na1.7, an attractive pain target. This mutant chimera enabled us to determine the cryoelectron microscopy (cryo-EM) structure of the channel functionally arrested by tarantula toxin. Our structure reveals a high-affinity resting-state-specific toxin-channel interaction between a key lysine residue that serves as a "stinger" and penetrates a triad of carboxyl groups in the S3-S4 linker of the voltage sensor. By unveiling this high-affinity binding mode, our studies establish a high-resolution channel-docking and resting-state locking mechanism for huwentoxin-IV and provide guidance for developing future resting-state-targeted analgesic drugs. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22661.map.gz | 59.3 MB | EMDB map data format | |
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Header (meta data) | emd-22661-v30.xml emd-22661.xml | 27.7 KB 27.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_22661_fsc.xml | 8.1 KB | Display | FSC data file |
Images | emd_22661.png | 153.1 KB | ||
Masks | emd_22661_msk_1.map | 64 MB | Mask map | |
Others | emd_22661_additional_1.map.gz emd_22661_additional_2.map.gz emd_22661_half_map_1.map.gz emd_22661_half_map_2.map.gz | 59.3 MB 58.7 MB 11 MB 11 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22661 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22661 | HTTPS FTP |
-Validation report
Summary document | emd_22661_validation.pdf.gz | 745.3 KB | Display | EMDB validaton report |
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Full document | emd_22661_full_validation.pdf.gz | 744.9 KB | Display | |
Data in XML | emd_22661_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | emd_22661_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22661 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22661 | HTTPS FTP |
-Related structure data
Related structure data | 7k48MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22661.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | EM map without post-cut-off B-factor sharpening | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.056 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_22661_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: EM map with post-cut-off B-factor sharpening of -50 A2.
File | emd_22661_additional_1.map | ||||||||||||
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Annotation | EM map with post-cut-off B-factor sharpening of -50 A2. | ||||||||||||
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Density Histograms |
-Additional map: EM full map
File | emd_22661_additional_2.map | ||||||||||||
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Annotation | EM full map | ||||||||||||
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Density Histograms |
-Half map: EM half map (odd)
File | emd_22661_half_map_1.map | ||||||||||||
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Annotation | EM half map (odd) | ||||||||||||
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Density Histograms |
-Half map: EM half map (even)
File | emd_22661_half_map_2.map | ||||||||||||
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Annotation | EM half map (even) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of NavAb/Nav1.7-VS2A chimera and m3-Huwentoxin-IV
Entire | Name: Complex of NavAb/Nav1.7-VS2A chimera and m3-Huwentoxin-IV |
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Components |
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-Supramolecule #1: Complex of NavAb/Nav1.7-VS2A chimera and m3-Huwentoxin-IV
Supramolecule | Name: Complex of NavAb/Nav1.7-VS2A chimera and m3-Huwentoxin-IV type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 300 KDa |
-Supramolecule #2: NavAb/Nav1.7-VS2A chimera
Supramolecule | Name: NavAb/Nav1.7-VS2A chimera / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: K12 |
-Supramolecule #3: m3-Huwentoxin-IV
Supramolecule | Name: m3-Huwentoxin-IV / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Haplopelma schmidti (Chinese earth tiger) |
Recombinant expression | Organism: synthetic construct (others) |
-Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,Ion transport pr...
Macromolecule | Name: Maltose/maltodextrin-binding periplasmic protein,Ion transport protein,Sodium channel protein type 9 subunit alpha chimera type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Arcobacter butzleri (strain RM4018) (bacteria) / Strain: RM4018 |
Molecular weight | Theoretical: 68.519062 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY ...String: MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFGG YAQSGLLAEI TPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE LKAKGKSALM FNLQEPYFTW P LIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NKGETAMTIN GPWAWSNIDT SK VNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPLGAVALKS YEEELAKDPR IAA TMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TNAMYLAITN IVESSFFTKF ITICIVLNTL FMAM EHHPM TEEFKNVLAI GNLVFTGIFA AEIILRIYVH RISFFKDPWS LFDFFVVTLS LVELFLADVE GLSVLRSFRL LRLFR AVTA VPQMRKIVSA LISVIPGMLS VIALMTLFFY IFAIMATQLF GERFPEWFGT LGESFYTLFQ VMTLESWSMG IVRPLM EVY PYAWVFFIPF IFVVTFVMIN LVVAIIVDAM AILNQKEEQH IIDEVQSH |
-Macromolecule #2: Mu-theraphotoxin-Hs2a
Macromolecule | Name: Mu-theraphotoxin-Hs2a / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Haplopelma schmidti (Chinese earth tiger) |
Molecular weight | Theoretical: 3.999777 KDa |
Sequence | String: GCLGIFKACN PSNDQCCKSS KLVCSRKTRW CKWQI |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 2.5-4.0 seconds before plunging. | ||||||||||||
Details | m3-HwTx-IV was added in excess to the chimera at 8:1 stoichiometric molar ratio of toxin to channel. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 70.0 K / Max: 70.0 K |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Details | Preliminary grid screening was performed manually. |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3582 pixel / Digitization - Frames/image: 2-42 / Number real images: 7168 / Average exposure time: 8.6 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |