Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the arylsulfonamide inhibitor GNE-3565. Determined by electron microscopy at 2.9 Å resolution. Released 12 Apr 2023.
Explore 8F0R in 3D Show helices and sheets RCSB PDB PDBe
8F0R contains 73 α-helices and 10 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 130-138 | 9 | |
| α-helix | 140-158 | 19 | |
| α-helix | 160-161 | 2 | |
| α-helix | 163-186 | 24 | |
| α-helix | 196-198 | 3 | |
| α-helix | 200-217 | 18 | |
| α-helix | 227-239 | 13 | |
| α-helix | 244-257 | 14 | |
| α-helix | 259-280 | 22 | |
| α-helix | 283-285 | 3 | |
| β-strand | 287-290 | 4 | 1 |
| α-helix | 291-293 | 3 | |
| α-helix | 303-311 | 9 | |
| α-helix | 313-315 | 3 | |
| β-strand | 316 | 1 | 1 |
| α-helix | 325-327 | 3 | |
| α-helix | 337-338 | 2 | |
| β-strand | 341-344 | 4 | 1 |
| α-helix | 361-373 | 13 | |
| α-helix | 377-388 | 12 | |
| α-helix | 390-392 | 3 | |
| α-helix | 393-399 | 7 | |
| α-helix | 400-407 | 8 | |
| α-helix | 408-429 | 22 | |
| α-helix | 519-537 | 19 | |
| α-helix | 545-572 | 28 | |
| α-helix | 575-580 | 6 | |
| α-helix | 582-599 | 18 | |
| α-helix | 610-613 | 4 | |
| α-helix | 614-618 | 5 | |
| α-helix | 620-623 | 4 | |
| α-helix | 625-636 | 12 | |
| α-helix | 638-669 | 32 | |
| α-helix | 671-673 | 3 | |
| α-helix | 687-699 | 13 | |
| α-helix | 703-712 | 10 | |
| α-helix | 717-727 | 11 | |
| α-helix | 728-732 | 5 | |
| α-helix | 733-743 | 11 | |
| α-helix | 843-853 | 11 | |
| α-helix | 856-873 | 18 | |
| α-helix | 880-882 | 3 | |
| α-helix | 884-912 | 29 | |
| α-helix | 914-918 | 5 | |
| α-helix | 921-942 | 22 | |
| α-helix | 944-947 | 4 | |
| α-helix | 948-952 | 5 | |
| α-helix | 953-958 | 6 | |
| α-helix | 959-963 | 5 | |
| α-helix | 969-1004 | 36 | |
| β-strand | 1009-1012 | 4 | 2 |
| β-strand | 1018 | 1 | 2 |
| α-helix | 1019-1020 | 2 | |
| β-strand | 1026 | 1 | 3 |
| α-helix | 1027-1032 | 6 | |
| β-strand | 1036-1039 | 4 | 2 |
| α-helix | 1047-1059 | 13 | |
| α-helix | 1063-1071 | 9 | |
| β-strand | 1078 | 1 | 3 |
| α-helix | 1086-1088 | 3 | |
| α-helix | 1089-1095 | 7 | |
| α-helix | 1096-1103 | 8 | |
| α-helix | 1106-1122 | 17 | |
| α-helix | 1131-1144 | 14 | |
| α-helix | 1158-1168 | 11 | |
| α-helix | 1170-1189 | 20 | |
| α-helix | 1196-1224 | 29 | |
| α-helix | 1227-1230 | 4 | |
| α-helix | 1232-1256 | 25 | |
| α-helix | 1261-1267 | 7 | |
| α-helix | 1268-1271 | 4 | |
| α-helix | 1272-1275 | 4 | |
| α-helix | 1276-1279 | 4 | |
| α-helix | 1284-1320 | 37 | |
| α-helix | 1339-1349 | 11 | |
| α-helix | 1355-1362 | 8 | |
| α-helix | 1369-1371 | 3 | |
| β-strand | 1372 | 1 | 4 |
| β-strand | 1377 | 1 | 4 |
| α-helix | 1384-1394 | 11 | |
| α-helix | 1395-1402 | 8 | |
| α-helix | 1403-1422 | 20 | |
| α-helix | 1427-1436 | 10 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera | A | protein | 1608 | Homo sapiens, Periplaneta americana | D0E0C2 (AlphaFold model), Q15858 (AlphaFold model) |
>8F0R_1 Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera (chains A) MWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSGGDYKDDDDKGGSGGDYKDDDDKMADNS PLIREERQRLFRPYTRAMLTAPSAQPAKENGKTEENKDNSRDKGRGANKDRDGSAHPDQA LEQGSRLPARMRNIFPAELASTPLEDFDPFYKNKKTFVVVTKAGDIFRFSGEKSLWMLDP FTPIRRVAISTMVQPIFSYFIMITILIHCIFMIMPATQTTYILELVFLSIYTIEVVVKVL ARGFILHPFAYLRDPWNWLDFLVTLIGYITLVVDLGHLYALRAFRVLRSWRTVTIVPGWR TIVDALSLSITSLKDLVLLLLFSLSVFALIGLQLFMGNLKHKCVKHFPADGSWGNFTDER WFNYTSNSSHWYIPDDWIEYPLCGNSSGAGMCPPGYTCLQGYGGNPNYGYTSFDTFGWAF LSVFRLVTLDYWEDLYQLALRSAGPWHILFFIIVVFYGTFCFLNFILAVVVMSYTHMVKR ADEEKAAERELKKEKKAASVANNTANGQEQTTIEMNGDEAVVIDNNDQAARQQSDPETPA PSVTQRLTDFLCVWDCCVPWQKLQGAIGAVVLSPFFELFIAVIIVLNITFMALDHHDMNI EFERILRTGNYIFTSIYIVEAVLKIIALSPKFYFKDSWNVFDFIIVVFAILELGLEGVQG LSVFRSFRLLRVFRLAKFWPTLNNFMSVMTKSYGAFVNVMYVMFLLLFIFAIIGMQLFGM NYIDNMERFPDGDLPRWNFTDFLHSFMIVFRALCGEWIESMWDCMLVGDWSCIPFFVAVF FVGNLVILNLLIALLLNNYGSFCTSPTSDEEDSKDEDALAQIVRIFKRFKPNLNAVKLSP MKPDSEDIVESQEIQGNNIADAEDVLAGEFPPDCCCNAFYKCFPSRPARDSSVQRMWSNI RRVCFLLAKNKYFQKFVTAVLVITSVLLALEDIYLPQRPVLVNITLYVDYVLTAFFVIEM IIMLFAVGFKKYFTSKWYWLDFIVVVAYLLNFVLMCAGIEALQTLRLLRVFRLFRPLSKV NGMQVVTSTLVEAVPHIFNVILVGIFFWLVFAIMGVQLFAGKFYKCVDENSTVLSHEITM DRNDCLHENYTWENSPMNFDHVGNAYLSLLQVATFKGWLQIMNDAIDSREVHKQPIRETN IYMYLYFIFFIVFGSFFILKLFVCILIDIFRQQRRKAEGLSATDSRTQLIYRRAVMRTMS AKPVKRIPKPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTEVLYWI NVVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFR VIRLARIGRILRLVKGAKGIRLLLLALRKALRTLFNVSFLLFVIMFVYAVFGMEFFMHIR DAGAIDDVYNFKTFGQSIILLFQLATSAGWDGVYFAIANEEDCRAPDHELGYPGNCGSRA LGIAYLVSYLIITCLVVINMYAAVILDYVLEVYEDSKEGLTDDDYDMFFEVWQQFDPEAT QYIRYDQLSELLEALQPPLQVQKPNKYKILSMNIPICKDDHIFYKDVLEALVKDVFSRRG SPVEAGDVQAPNVDEAEYKPVSSTLQRQREEYCVRLIQNAWRKHKQQN
| ID | Name | Formula | Copies |
|---|---|---|---|
| Y01 | Cholesterol hemisuccinate | C31 H50 O4 | 1 |
| PEE | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine | C41 H78 N O8 P | 2 |
| X7W | 5-chloro-4-({(1S,2S,4S)-2-(dimethylamino)-4-[3-(trifluoromethyl)phenyl]cyclohex… | C25 H26 Cl F4 N5 O2 S | 1 |
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 5 |
Cryo-EM reveals an unprecedented binding site for Na V 1.7 inhibitors enabling rational design of potent hybrid inhibitors. Kschonsak, M., Jao, C.C., Arthur, C.P. et al. Elife (2023) 12. DOI 10.7554/eLife.84151 · PubMed
Other PDB entries of the same protein (UniProt D0E0C2 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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