6A91: Sodium channel protein PaFPC1

Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana bound with saxitoxin and Dc1a. Determined by electron microscopy at 3.2 Å resolution. Released 8 Aug 2018.

Method
Electron microscopy
Resolution
3.2 Å
Organisms
Periplaneta americana, Diguetia canities
Chains
2
Atoms
11,182
Mol. weight
193.77 kDa
Ligands
9SL, PC1, NAG
Released
8 Aug 2018

Explore 6A91 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6A91 contains 88 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.

Chain A: 88 helices, 16 β-strands

ElementResiduesLengthSheet
α-helix48-558
α-helix95-1028
α-helix130-1378
α-helix140-15314
α-helix155-1584
α-helix160-1612
α-helix169-1768
α-helix179-1857
α-helix202-21413
α-helix224-24017
α-helix245-25713
α-helix259-28022
α-helix283-2853
β-strand287-28821
β-strand28912
α-helix290-2934
α-helix306-3094
α-helix313-3153
β-strand31612
β-strand32711
β-strand343-34421
α-helix352-3543
α-helix361-37313
α-helix378-3858
α-helix390-3923
α-helix393-4008
α-helix401-4066
α-helix409-42416
α-helix425-4273
α-helix430-4334
α-helix505-51511
α-helix519-53618
β-strand54313
α-helix545-57228
α-helix582-59716
α-helix615-6228
α-helix625-63612
α-helix638-66326
α-helix666-6694
α-helix671-6733
α-helix675-6773
α-helix687-69812
α-helix703-71210
α-helix717-72711
α-helix728-7325
α-helix733-74311
α-helix839-85416
α-helix858-87114
α-helix872-8754
α-helix880-8823
α-helix884-90926
α-helix913-9175
α-helix921-94121
α-helix944-9474
α-helix951-9577
α-helix968-97710
α-helix979-100426
β-strand1009-101244
α-helix10171
β-strand101814
α-helix10191
β-strand102615
α-helix1027-10315
β-strand1036-103944
α-helix10401
α-helix1047-105610
α-helix1063-107210
β-strand107815
α-helix1086-10883
α-helix1089-10968
α-helix1097-11015
α-helix1106-112217
α-helix1125-11262
α-helix1133-11408
α-helix1150-11556
α-helix1160-11645
α-helix1170-11756
α-helix1178-11847
α-helix1187-11893
α-helix1198-122225
α-helix1228-12303
α-helix1232-124817
α-helix1261-12699
α-helix1270-12778
α-helix1283-129311
α-helix1296-132025
β-strand132716
β-strand133016
α-helix1339-134810
α-helix1349-13513
α-helix1355-13628
α-helix1384-139411
α-helix1395-13995
α-helix1400-14012
α-helix1403-142119
α-helix1427-143711
β-strand1447-144937
α-helix1450-14523
α-helix1453-14597
α-helix1471-14755
β-strand148217
β-strand1486-148837
α-helix1490-150415
α-helix1510-152011
Chain B: 0 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand6-838
β-strand1913
β-strand28-3038
β-strand35-3738
β-strand38-4253
β-strand52-5653

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein PaFPC1Aprotein1596Periplaneta americanaD0E0C2 (AlphaFold model)
Mu-diguetoxin-Dc1aBprotein57Diguetia canitiesP49126 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6A91_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
Sequence of entity 2 (B), FASTA
>6A91_2 Mu-diguetoxin-Dc1a (chains B)
SAKDGDVEGPAGCKKYDVECDSGECCQKQYLWYKWRPLDCRCLKSGFFSSKCVCRDV

Ligands and cofactors

IDNameFormulaCopies
9SL[(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1…C10 H17 N7 O41
PC11,2-diacyl-sn-glycero-3-phosphocholineC44 H88 N O8 P2
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O63

Primary citation

Structural basis for the modulation of voltage-gated sodium channels by animal toxins. Shen, H., Li, Z., Jiang, Y. et al. Science (2018) 362. DOI 10.1126/science.aau2596 · PubMed

Other PDB entries of the same protein (UniProt D0E0C2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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