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Yorodumi- EMDB-28779: Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28779 | |||||||||
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Title | Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296 | |||||||||
Map data | Density modified map used for model refinements | |||||||||
Sample |
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Function / homology | Function and homology information detection of mechanical stimulus involved in sensory perception / voltage-gated sodium channel complex / host cell presynaptic membrane / high voltage-gated calcium channel activity / voltage-gated sodium channel activity / Interaction between L1 and Ankyrins / sodium ion transport / behavioral response to pain / voltage-gated calcium channel complex / Phase 0 - rapid depolarisation ...detection of mechanical stimulus involved in sensory perception / voltage-gated sodium channel complex / host cell presynaptic membrane / high voltage-gated calcium channel activity / voltage-gated sodium channel activity / Interaction between L1 and Ankyrins / sodium ion transport / behavioral response to pain / voltage-gated calcium channel complex / Phase 0 - rapid depolarisation / detection of temperature stimulus involved in sensory perception of pain / calcium ion import across plasma membrane / sodium ion transmembrane transport / sodium channel regulator activity / sensory perception of pain / post-embryonic development / Sensory perception of sweet, bitter, and umami (glutamate) taste / response to toxic substance / circadian rhythm / toxin activity / inflammatory response / axon / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Diguetia canities (spider) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Kschonsak M / Jao CC / Arthur CP / Rohou AL / Bergeron P / Ortwine D / McKerall SJ / Hackos DH / Deng L / Chen J ...Kschonsak M / Jao CC / Arthur CP / Rohou AL / Bergeron P / Ortwine D / McKerall SJ / Hackos DH / Deng L / Chen J / Sutherlin D / Dragovich PS / Volgraf M / Wright MR / Payandeh J / Ciferri C / Tellis JC | |||||||||
Funding support | 1 items
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Citation | Journal: Elife / Year: 2023 Title: Cryo-EM reveals an unprecedented binding site for Na1.7 inhibitors enabling rational design of potent hybrid inhibitors. Authors: Marc Kschonsak / Christine C Jao / Christopher P Arthur / Alexis L Rohou / Philippe Bergeron / Daniel F Ortwine / Steven J McKerrall / David H Hackos / Lunbin Deng / Jun Chen / Tianbo Li / ...Authors: Marc Kschonsak / Christine C Jao / Christopher P Arthur / Alexis L Rohou / Philippe Bergeron / Daniel F Ortwine / Steven J McKerrall / David H Hackos / Lunbin Deng / Jun Chen / Tianbo Li / Peter S Dragovich / Matthew Volgraf / Matthew R Wright / Jian Payandeh / Claudio Ciferri / John C Tellis / Abstract: The voltage-gated sodium (Na) channel Na1.7 has been identified as a potential novel analgesic target due to its involvement in human pain syndromes. However, clinically available Na channel-blocking ...The voltage-gated sodium (Na) channel Na1.7 has been identified as a potential novel analgesic target due to its involvement in human pain syndromes. However, clinically available Na channel-blocking drugs are not selective among the nine Na channel subtypes, Na1.1-Na1.9. Moreover, the two currently known classes of Na1.7 subtype-selective inhibitors (aryl- and acylsulfonamides) have undesirable characteristics that may limit their development. To this point understanding of the structure-activity relationships of the acylsulfonamide class of Na1.7 inhibitors, exemplified by the clinical development candidate , has been based solely on a single co-crystal structure of an arylsulfonamide inhibitor bound to voltage-sensing domain 4 (VSD4). To advance inhibitor design targeting the Na1.7 channel, we pursued high-resolution ligand-bound Na1.7-VSD4 structures using cryogenic electron microscopy (cryo-EM). Here, we report that engages the Na1.7-VSD4 through an unexpected binding mode orthogonal to the arylsulfonamide inhibitor class binding pose, which identifies a previously unknown ligand binding site in Na channels. This finding enabled the design of a novel hybrid inhibitor series that bridges the aryl- and acylsulfonamide binding pockets and allows for the generation of molecules with substantially differentiated structures and properties. Overall, our study highlights the power of cryo-EM methods to pursue challenging drug targets using iterative and high-resolution structure-guided inhibitor design. This work also underscores an important role of the membrane bilayer in the optimization of selective Na channel modulators targeting VSD4. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28779.map.gz | 7.8 MB | EMDB map data format | |
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Header (meta data) | emd-28779-v30.xml emd-28779.xml | 24.3 KB 24.3 KB | Display Display | EMDB header |
Images | emd_28779.png | 82.5 KB | ||
Others | emd_28779_additional_1.map.gz emd_28779_half_map_1.map.gz emd_28779_half_map_2.map.gz | 226.2 MB 49 MB 49 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28779 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28779 | HTTPS FTP |
-Related structure data
Related structure data | 8f0sMC 8f0pC 8f0qC 8f0rC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28779.map.gz / Format: CCP4 / Size: 8.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Density modified map used for model refinements | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.824 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Non-modified, full map
File | emd_28779_additional_1.map | ||||||||||||
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Annotation | Non-modified, full map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map-1
File | emd_28779_half_map_1.map | ||||||||||||
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Annotation | half-map-1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map-2
File | emd_28779_half_map_2.map | ||||||||||||
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Annotation | half-map-2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor ...
Entire | Name: VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296 |
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Components |
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-Supramolecule #1: VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor ...
Supramolecule | Name: VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296 type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 Details: Chimeric construct of human Nav1.7 VSD4 and the NavPaS channel from American cockroach Periplaneta americana |
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Source (natural) | Organism: Homo sapiens (human) |
-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 chimera type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 184.481906 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MWSHPQFEKG GGSGGGSGGS AWSHPQFEKG GSGGDYKDDD DKGGSGGDYK DDDDKMADNS PLIREERQRL FRPYTRAMLT APSAQPAKE NGKTEENKDN SRDKGRGANK DRDGSAHPDQ ALEQGSRLPA RMRNIFPAEL ASTPLEDFDP FYKNKKTFVV V TKAGDIFR ...String: MWSHPQFEKG GGSGGGSGGS AWSHPQFEKG GSGGDYKDDD DKGGSGGDYK DDDDKMADNS PLIREERQRL FRPYTRAMLT APSAQPAKE NGKTEENKDN SRDKGRGANK DRDGSAHPDQ ALEQGSRLPA RMRNIFPAEL ASTPLEDFDP FYKNKKTFVV V TKAGDIFR FSGEKSLWML DPFTPIRRVA ISTMVQPIFS YFIMITILIH CIFMIMPATQ TTYILELVFL SIYTIEVVVK VL ARGFILH PFAYLRDPWN WLDFLVTLIG YITLVVDLGH LYALRAFRVL RSWRTVTIVP GWRTIVDALS LSITSLKDLV LLL LFSLSV FALIGLQLFM GNLKHKCVKH FPADGSWGNF TDERWFNYTS NSSHWYIPDD WIEYPLCGNS SGAGMCPPGY TCLQ GYGGN PNYGYTSFDT FGWAFLSVFR LVTLDYWEDL YQLALRSAGP WHILFFIIVV FYGTFCFLNF ILAVVVMSYT HMVKR ADEE KAAERELKKE KKAASVANNT ANGQEQTTIE MNGDEAVVID NNDQAARQQS DPETPAPSVT QRLTDFLCVW DCCVPW QKL QGAIGAVVLS PFFELFIAVI IVLNITFMAL DHHDMNIEFE RILRTGNYIF TSIYIVEAVL KIIALSPKFY FKDSWNV FD FIIVVFAILE LGLEGVQGLS VFRSFRLLRV FRLAKFWPTL NNFMSVMTKS YGAFVNVMYV MFLLLFIFAI IGMQLFGM N YIDNMERFPD GDLPRWNFTD FLHSFMIVFR ALCGEWIESM WDCMLVGDWS CIPFFVAVFF VGNLVILNLL IALLLNNYG SFCTSPTSDE EDSKDEDALA QIVRIFKRFK PNLNAVKLSP MKPDSEDIVE SQEIQGNNIA DAEDVLAGEF PPDCCCNAFY KCFPSRPAR DSSVQRMWSN IRRVCFLLAK NKYFQKFVTA VLVITSVLLA LEDIYLPQRP VLVNITLYVD YVLTAFFVIE M IIMLFAVG FKKYFTSKWY WLDFIVVVAY LLNFVLMCAG IEALQTLRLL RVFRLFRPLS KVNGMQVVTS TLVEAVPHIF NV ILVGIFF WLVFAIMGVQ LFAGKFYKCV DENSTVLSHE ITMDRNDCLH ENYTWENSPM NFDHVGNAYL SLLQVATFKG WLQ IMNDAI DSREVHKQPI RETNIYMYLY FIFFIVFGSF FILKLFVCIL IDIFRQQRRK AEGLSATDSR TQLIYRRAVM RTMS AKPVK RIPKPGNKIQ GCIFDLVTNQ AFDISIMVLI CLNMVTMMVE KEGQSQHMTE VLYWINVVFI ILFTGECVLK LISLR HYYF TVGWNIFDFV VVIISIVGMF LADLIETYFV SPTLFRVIRL ARIGRILRLV KGAKGIRLLL LALRKALRTL FNVSFL LFV IMFVYAVFGM EFFMHIRDAG AIDDVYNFKT FGQSIILLFQ LATSAGWDGV YFAIANEEDC RAPDHELGYP GNCGSRA LG IAYLVSYLII TCLVVINMYA AVILDYVLEV YEDSKEGLTD DDYDMFFEVW QQFDPEATQY IRYDQLSELL EALQPPLQ V QKPNKYKILS MNIPICKDDH IFYKDVLEAL VKDVFSRRGS PVEAGDVQAP NVDEAEYKPV SSTLQRQREE YCVRLIQNA WRKHKQQN |
-Macromolecule #2: Beta-diguetoxin-Dc1a
Macromolecule | Name: Beta-diguetoxin-Dc1a / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Diguetia canities (spider) |
Molecular weight | Theoretical: 8.240277 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: HHHHHHGENL YFQGSAKDGD VEGPAGCKKY DVECDSGECC QKQYLWYKWR PLDCRCLKSG FFSSKCVCRD V |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #6: 5-chloro-4-(cyclopentylmethoxy)-N-(4-{[(1S,2S)-2-(dimethylamino)c...
Macromolecule | Name: 5-chloro-4-(cyclopentylmethoxy)-N-(4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonyl)-2-fluorobenzamide type: ligand / ID: 6 / Number of copies: 1 / Formula: X80 |
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Molecular weight | Theoretical: 570.091 Da |
Chemical component information | ChemComp-X80: |
-Macromolecule #7: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Macromolecule | Name: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / type: ligand / ID: 7 / Number of copies: 1 / Formula: PEE |
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Molecular weight | Theoretical: 744.034 Da |
Chemical component information | ChemComp-PEE: |
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec. | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | The sample was monodisperse. The sample was crosslinked with 0.05% glutaraldehyde for 10 minutes at RT, then quenched with 1M Tris pH7.0. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1774062 Details: template-matching particle picking with a 30A low-pass filtered template |
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Initial angle assignment | Type: OTHER / Software - Name: cisTEM (ver. 1.02) |
Final 3D classification | Number classes: 100 / Avg.num./class: 17741 / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: OTHER / Software - Name: cisTEM (ver. 1.02) / Details: No data beyond 4.0 A were used in the refinements |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX (ver. 1.20) / Number images used: 826525 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-8f0s: |