Structure of the voltage-gated sodium channel NavPas from American Cockroach Periplaneta Americana in complex with scorpion alpha-toxin LqhaIT. Determined by electron microscopy at 3.9 Å resolution. Released 4 Sept 2024.
Explore 8VQC in 3D Show helices and sheets RCSB PDB PDBe
8VQC contains 68 α-helices and 22 β-strands across 2 chains. 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 |
|---|---|---|---|
| β-strand | 63 | 1 | 1 |
| β-strand | 65 | 1 | 2 |
| β-strand | 74 | 1 | 2 |
| α-helix | 95-110 | 16 | |
| β-strand | 119 | 1 | 1 |
| α-helix | 129-138 | 10 | |
| α-helix | 140-156 | 17 | |
| α-helix | 166-187 | 22 | |
| α-helix | 192-196 | 5 | |
| α-helix | 200-215 | 16 | |
| α-helix | 229-239 | 11 | |
| α-helix | 244-279 | 36 | |
| β-strand | 287 | 1 | 3 |
| β-strand | 289-290 | 2 | 4 |
| α-helix | 293 | 1 | |
| α-helix | 304-310 | 7 | |
| β-strand | 316 | 1 | 4 |
| β-strand | 327 | 1 | 3 |
| α-helix | 337-338 | 2 | |
| β-strand | 341-342 | 2 | 4 |
| α-helix | 361-372 | 12 | |
| α-helix | 377-388 | 12 | |
| α-helix | 390-392 | 3 | |
| α-helix | 393-399 | 7 | |
| α-helix | 400-404 | 5 | |
| α-helix | 405-430 | 26 | |
| α-helix | 503-517 | 15 | |
| α-helix | 519-536 | 18 | |
| α-helix | 545-572 | 28 | |
| α-helix | 575-578 | 4 | |
| α-helix | 582-600 | 19 | |
| α-helix | 609-612 | 4 | |
| α-helix | 615-618 | 4 | |
| α-helix | 619-622 | 4 | |
| α-helix | 627-635 | 9 | |
| α-helix | 638-669 | 32 | |
| α-helix | 687-699 | 13 | |
| α-helix | 703-711 | 9 | |
| α-helix | 715-717 | 3 | |
| α-helix | 718-726 | 9 | |
| α-helix | 728-733 | 6 | |
| α-helix | 734-743 | 10 | |
| α-helix | 834-854 | 21 | |
| α-helix | 856-874 | 19 | |
| α-helix | 884-911 | 28 | |
| α-helix | 914-919 | 6 | |
| α-helix | 921-941 | 21 | |
| α-helix | 954-957 | 4 | |
| α-helix | 959-962 | 4 | |
| α-helix | 968-1004 | 37 | |
| β-strand | 1009-1012 | 4 | 5 |
| β-strand | 1026 | 1 | 6 |
| α-helix | 1027-1032 | 6 | |
| β-strand | 1036-1039 | 4 | 5 |
| α-helix | 1047-1058 | 12 | |
| α-helix | 1063-1070 | 8 | |
| β-strand | 1078 | 1 | 6 |
| α-helix | 1089-1096 | 8 | |
| α-helix | 1100-1104 | 5 | |
| α-helix | 1106-1123 | 18 | |
| α-helix | 1132-1145 | 14 | |
| α-helix | 1158-1167 | 10 | |
| α-helix | 1170-1188 | 19 | |
| α-helix | 1196-1223 | 28 | |
| α-helix | 1235-1256 | 22 | |
| α-helix | 1260-1267 | 8 | |
| α-helix | 1268-1272 | 5 | |
| α-helix | 1283-1294 | 12 | |
| α-helix | 1296-1320 | 25 | |
| α-helix | 1339-1350 | 12 | |
| α-helix | 1355-1362 | 8 | |
| α-helix | 1385-1394 | 10 | |
| α-helix | 1395-1402 | 8 | |
| α-helix | 1403-1423 | 21 | |
| α-helix | 1427-1438 | 12 | |
| α-helix | 1452-1458 | 7 | |
| α-helix | 1465-1467 | 3 | |
| α-helix | 1471-1476 | 6 | |
| β-strand | 1482 | 1 | 7 |
| β-strand | 1486 | 1 | 7 |
| α-helix | 1489-1504 | 16 | |
| α-helix | 1509-1520 | 12 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2 | 1 | 8 |
| β-strand | 5 | 1 | 9 |
| β-strand | 6 | 1 | 10 |
| α-helix | 19-28 | 10 | |
| β-strand | 34-35 | 2 | 9 |
| β-strand | 47-48 | 2 | 9 |
| β-strand | 51 | 1 | 8 |
| β-strand | 57 | 1 | 10 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Sodium channel protein PaFPC1 | A | protein | 1596 | Periplaneta americana | D0E0C2 (AlphaFold model) |
| Alpha-insect toxin LqhaIT | H | protein | 65 | Leiurus quinquestriatus hebraeus | P17728 (AlphaFold model) |
>8VQC_1 Sodium channel protein PaFPC1 (chains A) MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMADNSPLIREERQRLFR PYTRAMLTAPSAQPAKENGKTEENKDNSRDKGRGANKDRDGSAHPDQALEQGSRLPARMR NIFPAELASTPLEDFDPFYKNKKTFVVVTKAGDIFRFSGEKSLWMLDPFTPIRRVAISTM VQPIFSYFIMITILIHCIFMIMPATQTTYILELVFLSIYTIEVVVKVLARGFILHPFAYL RDPWNWLDFLVTLIGYITLVVDLGHLYALRAFRVLRSWRTVTIVPGWRTIVDALSLSITS LKDLVLLLLFSLFVFAVLGLQIYMGVLTQKCVKHFPADGSWGNFTDERWFNYTSNSSHWY IPDDWIEYPLCGNSSGAGMCPPGYTCLQGYGGNPNYGYTSFDTFGWAFLSVFRLVTLDYW EDLYQLALRSAGPWHILFFIIVVFYGTFCFLNFILAVVVMSYTHMVKRADEEKAAERELK KEKKAASVANNTANGQEQTTIEMNGDEAVVIDNNDQAARQQSDPETPAPSVTQRLTDFLC VWDCCVPWQKLQGAIGAVVLSPFFELFIAVIIVLNITFMALDHHDMNIEFERILRTGNYI FTSIYIVEAVLKIIALSPKFYFKDSWNVFDFIIVVFAILELGLEGVQGLSVFRSFRLLRV FRLAKFWPTLNNFMSVMTKSYGAFVNVMYVMFLLLFIFAIIGMQLFGMNYIDNMERFPDG DLPRWNFTDFLHSFMIVFRALCGEWIESMWDCMLVGDWSCIPFFVAVFFVGNLVILNLLI ALLLNNYGSFCTSPTSDEEDSKDEDALAQIVRIFKRFKPNLNAVKLSPMKPDSEDIVESQ EIQGNNIADAEDVLAGEFPPDCCCNAFYKCFPSRPARDSSVQRMWSNIRRVCFLLAKNKY FQKFVTAVLVITSVLLALEDIYLPQRPVLVNITLYVDYVLTAFFVIEMIIMLFAVGFKKY FTSKWYWLDFIVVVAYLLNFVLMCAGIEALQTLRLLRVFRLFRPLSKVNGMQVVTSTLVE AVPHIFNVILVGIFFWLVFAIMGVQLFAGKFYKCVDENSTVLSHEITMDRNDCLHENYTW ENSPMNFDHVGNAYLSLLQVATFKGWLQIMNDAIDSREVHKQPIRETNIYMYLYFIFFIV FGSFFILKLFVCILIDIFRQQRRKAEGLSATDSRTQLIYRRAVMRTMSAKPVKRIPKPTC HPQSLMYDISVNRKFEYTMMILIILNVAVMAIDHYGQSMEFSEVLDYLNLIFIIIFFVEC VIKVSGLRHHYFKDPWNIIDFLYVVLAIAGLMLSDVIEKYFISPTLLRILRILRVGRLLR YFQSARGMRLLLLALRKALRTLFNVSFLLFVIMFVYAVFGMEFFMHIRDAGAIDDVYNFK TFGQSIILLFQLATSAGWDGVYFAIANEEDCRAPDHELGYPGNCGSRALGIAYLVSYLII TCLVVINMYAAVILDYVLEVYEDSKEGLTDDDYDMFFEVWQQFDPEATQYIRYDQLSELL EALQPPLQVQKPNKYKILSMNIPICKDDHIFYKDVLEALVKDVFSRRGSPVEAGDVQAPN VDEAEYKPVSSTLQRQREEYCVRLIQNAWRKHKQQN
>8VQC_2 Alpha-insect toxin LqhaIT (chains H) MVRDAYIAKNYNCVYECFRDAYCNELCTKNGASSGYCQWAGKYGNACWCYALPDNVPIRV PGKCR
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
Scorpion alpha-toxin Lqh alpha IT specifically interacts with a glycan at the pore domain of voltage-gated sodium channels. Phulera, S., Dickson, C.J., Schwalen, C.J. et al. Structure (2024) 32:1611-1620.e4. DOI 10.1016/j.str.2024.07.021 · 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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