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- EMDB-0501: Cryo-EM structure of a human-cockroach hybrid Nav channel bound t... -
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Basic information
Entry | Database: EMDB / ID: EMD-0501 | |||||||||
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Title | Cryo-EM structure of a human-cockroach hybrid Nav channel bound to alpha-scorpion toxin AaH2. | |||||||||
![]() | Sharpened and mask map used for model building. | |||||||||
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Function / homology | ![]() detection of mechanical stimulus involved in sensory perception / cardiac muscle cell action potential involved in contraction / sodium channel inhibitor activity / voltage-gated sodium channel complex / membrane depolarization during action potential / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / behavioral response to pain / Phase 0 - rapid depolarisation ...detection of mechanical stimulus involved in sensory perception / cardiac muscle cell action potential involved in contraction / sodium channel inhibitor activity / voltage-gated sodium channel complex / membrane depolarization during action potential / Interaction between L1 and Ankyrins / voltage-gated sodium channel activity / sodium ion transport / behavioral response to pain / Phase 0 - rapid depolarisation / detection of temperature stimulus involved in sensory perception of pain / sodium ion transmembrane transport / neuronal action potential / sensory perception of pain / post-embryonic development / response to toxic substance / Sensory perception of sweet, bitter, and umami (glutamate) taste / defense response / circadian rhythm / toxin activity / inflammatory response / axon / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Clairfeuille T / Rohou A / Payandeh J | |||||||||
![]() | ![]() Title: Structural basis of α-scorpion toxin action on Na channels. Authors: Thomas Clairfeuille / Alexander Cloake / Daniel T Infield / José P Llongueras / Christopher P Arthur / Zhong Rong Li / Yuwen Jian / Marie-France Martin-Eauclaire / Pierre E Bougis / Claudio ...Authors: Thomas Clairfeuille / Alexander Cloake / Daniel T Infield / José P Llongueras / Christopher P Arthur / Zhong Rong Li / Yuwen Jian / Marie-France Martin-Eauclaire / Pierre E Bougis / Claudio Ciferri / Christopher A Ahern / Frank Bosmans / David H Hackos / Alexis Rohou / Jian Payandeh / ![]() ![]() ![]() ![]() Abstract: Fast inactivation of voltage-gated sodium (Na) channels is essential for electrical signaling, but its mechanism remains poorly understood. Here we determined the structures of a eukaryotic Na ...Fast inactivation of voltage-gated sodium (Na) channels is essential for electrical signaling, but its mechanism remains poorly understood. Here we determined the structures of a eukaryotic Na channel alone and in complex with a lethal α-scorpion toxin, AaH2, by electron microscopy, both at 3.5-angstrom resolution. AaH2 wedges into voltage-sensing domain IV (VSD4) to impede fast activation by trapping a deactivated state in which gating charge interactions bridge to the acidic intracellular carboxyl-terminal domain. In the absence of AaH2, the S4 helix of VSD4 undergoes a ~13-angstrom translation to unlatch the intracellular fast-inactivation gating machinery. Highlighting the polypharmacology of α-scorpion toxins, AaH2 also targets an unanticipated receptor site on VSD1 and a pore glycan adjacent to VSD4. Overall, this work provides key insights into fast inactivation, electromechanical coupling, and pathogenic mutations in Na channels. | |||||||||
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 | ![]() | 55.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.3 KB 24.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.8 KB | Display | ![]() |
Images | ![]() | 149.9 KB | ||
Masks | ![]() | 59.6 MB | ![]() | |
Others | ![]() ![]() ![]() | 55.2 MB 12.9 MB 12.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 754.7 KB | Display | ![]() |
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Full document | ![]() | 754.3 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nt4MC ![]() 0500C ![]() 6nt3C C: citing same article ( M: atomic model generated by this map |
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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 | Sharpened and mask map used for model building. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Unsharpened and unmodified map straight out of cisTEM...
File | emd_0501_additional.map | ||||||||||||
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Annotation | Unsharpened and unmodified map straight out of cisTEM last local refinement round. | ||||||||||||
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Density Histograms |
-Half map: Halfmap 1
File | emd_0501_half_map_1.map | ||||||||||||
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Annotation | Halfmap 1 | ||||||||||||
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Density Histograms |
-Half map: Halfmap 2
File | emd_0501_half_map_2.map | ||||||||||||
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Annotation | Halfmap 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : NavPas-VSD4-AaH2
Entire | Name: NavPas-VSD4-AaH2 |
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Components |
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-Supramolecule #1: NavPas-VSD4-AaH2
Supramolecule | Name: NavPas-VSD4-AaH2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
Molecular weight | Theoretical: 155 KDa |
-Macromolecule #1: Sodium channel protein PaFPC1,Sodium channel protein type 9 subun...
Macromolecule | Name: Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha,Sodium channel protein PaFPC1 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 178.763656 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: WSHPQFEKGG GSGGGSGGSA WSHPQFEKGG SGGDYKDDDD KGGSGGDYKD DDDKMADNSP LIREERQRLF RPYTRAMLTA PSAQPAKEN GKTEENKDNS RDKGRGANKD RDGSAHPDQA LEQGSRLPAR MRNIFPAELA STPLEDFDPF YKNKKTFVVV T KAGDIFRF ...String: WSHPQFEKGG GSGGGSGGSA WSHPQFEKGG SGGDYKDDDD KGGSGGDYKD DDDKMADNSP LIREERQRLF RPYTRAMLTA PSAQPAKEN GKTEENKDNS RDKGRGANKD RDGSAHPDQA LEQGSRLPAR MRNIFPAELA STPLEDFDPF YKNKKTFVVV T KAGDIFRF SGEKSLWMLD PFTPIRRVAI STMVQPIFSY FIMITILIHC IFMIMPATQT TYILELVFLS IYTIEVVVKV LA RGFILHP FAYLRDPWNW LDFLVTLIGY ITLVVDLGHL YALRAFRVLR SWRTVTIVPG WRTIVDALSL SITSLKDLVL LLL FSLSVF ALIGLQLFMG NLKHKCVKHF PADGSWGNFT DERWFNYTSN SSHWYIPDDW IEYPLCGNSS GAGMCPPGYT CLQG YGGNP NYGYTSFDTF GWAFLSVFRL VTLDYWEDLY QLALRSAGPW HILFFIIVVF YGTFCFLNFI LAVVVMSYTH MVKRA DEEK AAERELKKEK KAASVANNTA NGQEQTTIEM NGDEAVVIDN NDQAARQQSD PETPAPSVTQ RLTDFLCVWD CCVPWQ KLQ GAIGAVVLSP FFELFIAVII VLNITFMALD HHDMNIEFER ILRTGNYIFT SIYIVEAVLK IIALSPKFYF KDSWNVF DF IIVVFAILEL GLEGVQGLSV FRSFRLLRVF RLAKFWPTLN NFMSVMTKSY GAFVNVMYVM FLLLFIFAII GMQLFGMN Y IDNMERFPDG DLPRWNFTDF LHSFMIVFRA LCGEWIESMW DCMLVGDWSC IPFFVAVFFV GNLVILNLLI ALLLNNYGS FCTSPTSDEE DSKDEDALAQ IVRIFKRFKP NLNAVKLSPM KPDSEDIVES QEIQGNNIAD AEDVLAGEFP PDCCCNAFYK CFPSRPARD SSVQRMWSNI RRVCFLLAKN KYFQKFVTAV LVITSVLLAL EDIYLPQRPV LVNITLYVDY VLTAFFVIEM I IMLFAVGF KKYFTSKWYW LDFIVVVAYL LNFVLMCAGI EALQTLRLLR VFRLFRPLSK VNGMQVVTST LVEAVPHIFN VI LVGIFFW LVFAIMGVQL FAGKFYKCVD ENSTVLSHEI TMDRNDCLHE NYTWENSPMN FDHVGNAYLS LLQVATFKGW LQI MNDAID SREVHKQPIR ETNIYMYLYF IFFIVFGSFF ILKLFVCILI DIFRQQRRKA EGLSATDSRT QLIYRRAVMR TMSA KPVKR IPKPGNKIQG CIFDLVTNQA FDISIMVLIC LNMVTMMVEK EGQSQHMTEV LYWINVVFII LFTGECVLKL ISLRH YYFT VGWNIFDFVV VIISIVGMFL ADLIETYFVS PTLFRVIRLA RIGRILRLVK GAKGIRLLLL ALRKALRTLF NVSFLL FVI MFVYAVFGME FFMHIRDAGA IDDVYNFKTF GQSIILLFQL ATSAGWDGVY FAIANEEDCR APDHELGYPG NCGSRAL GI AYLVSYLIIT CLVVINMYAA VILDYVLEVY EDSKEGLTDD DYDMFFEVWQ QFDPEATQYI RYDQLSELLE ALQPPLQV Q KPNKYKILSM NIPICKDDHI FYKDVLEALV KDVFSRRG |
-Macromolecule #2: Alpha-mammal toxin AaH2
Macromolecule | Name: Alpha-mammal toxin AaH2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.260175 KDa |
Sequence | String: VKDGYIVDDV NCTYFCGRNA YCNEECTKLK GESGYCQWAS PYGNACYCYK LPDHVRTKGP GRCH(NH2) |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #5: (7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24la...
Macromolecule | Name: (7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosphaheptacos-7-en-21-yl (9Z,12E)-octadeca-9,12-dienoate type: ligand / ID: 5 / Number of copies: 5 / Formula: 76F |
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Molecular weight | Theoretical: 742.018 Da |
Chemical component information | ![]() ChemComp-76F: |
-Macromolecule #6: Digitonin
Macromolecule | Name: Digitonin / type: ligand / ID: 6 / Number of copies: 1 / Formula: AJP |
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Molecular weight | Theoretical: 1.229312 KDa |
Chemical component information | ![]() ChemComp-AJP: |
-Macromolecule #7: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
Macromolecule | Name: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 7 / Number of copies: 1 / Formula: LHG |
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Molecular weight | Theoretical: 722.97 Da |
Chemical component information | ![]() ChemComp-LHG: |
-Macromolecule #8: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ![]() ChemComp-Y01: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING Details: Grids were plasma etched using the Solarus plasma cleaner (Gatan) in the hydrogen-oxygen setting. Grids were etched for 4 minutes on each side to remove burrs from hole edges. The grids were ...Details: Grids were plasma etched using the Solarus plasma cleaner (Gatan) in the hydrogen-oxygen setting. Grids were etched for 4 minutes on each side to remove burrs from hole edges. The grids were then coated on both sides with 5nm of Au/Pd which was plasma deposited using the Leica ACE600 (Leica). |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 14886 / Average exposure time: 10.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |