6A95: Sodium channel protein PaFPC1

Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana bound with tetrodotoxin and Dc1a. Determined by electron microscopy at 2.6 Å resolution. Released 8 Aug 2018.

Method
Electron microscopy
Resolution
2.6 Å
Organisms
Periplaneta americana, Diguetia canities
Chains
2
Atoms
11,002
Mol. weight
192.23 kDa
Ligands
9SR, NAG
Released
8 Aug 2018

Explore 6A95 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6A95 contains 87 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: 87 helices, 17 β-strands

ElementResiduesLengthSheet
α-helix52-554
α-helix128-13710
α-helix140-15314
α-helix155-1584
α-helix160-1612
α-helix163-18523
α-helix203-21412
α-helix226-24015
α-helix244-25613
α-helix259-28022
α-helix283-2853
β-strand286-28721
β-strand28912
β-strand29013
α-helix291-2933
α-helix303-3108
α-helix313-3153
β-strand31612
α-helix325-3262
β-strand32711
β-strand34113
β-strand344-34521
α-helix361-37212
α-helix377-38711
α-helix390-3923
α-helix393-40210
α-helix403-4075
α-helix408-43427
α-helix511-5166
α-helix519-53719
β-strand54314
α-helix546-56823
α-helix578-5803
α-helix584-59916
α-helix609-62214
α-helix625-63410
α-helix638-66326
α-helix666-6694
α-helix671-6733
α-helix675-6773
α-helix687-69812
α-helix703-71210
α-helix715-7173
α-helix718-7258
α-helix726-7327
α-helix733-7419
α-helix841-85414
α-helix856-87419
α-helix880-8823
α-helix884-91128
α-helix921-94020
α-helix945-9473
α-helix948-9514
α-helix952-9598
α-helix962-9643
α-helix968-9769
α-helix979-100426
β-strand1009-101245
α-helix10171
β-strand101815
α-helix1019-10202
β-strand102616
α-helix1027-10326
β-strand1036-103945
α-helix1047-105812
α-helix1063-107210
β-strand107816
α-helix1086-10883
α-helix1089-10957
α-helix1096-11049
α-helix1106-112217
α-helix1131-114313
α-helix1148-11547
α-helix1158-11658
α-helix1170-118516
α-helix1187-11893
α-helix1196-12049
α-helix1207-122216
α-helix1226-12305
α-helix1232-124817
α-helix1261-127010
α-helix1271-12744
α-helix1275-12784
α-helix1283-129412
α-helix1296-132025
α-helix1339-134810
α-helix1349-13513
α-helix1355-13628
α-helix1369-13713
β-strand137217
β-strand137717
α-helix1384-139411
α-helix1395-14028
α-helix1404-142219
α-helix1428-14369
β-strand1447-144938
α-helix1450-14523
α-helix1453-14586
α-helix1465-14673
α-helix1470-14745
α-helix1483-14853
β-strand1486-148838
α-helix1489-150315
α-helix1514-15196
Chain B: 0 helices, 5 β-strands
ElementResiduesLengthSheet
β-strand1914
β-strand28-3039
β-strand35-3739
β-strand38-4474
β-strand50-5674

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein PaFPC1Aprotein1596Periplaneta americanaD0E0C2 (AlphaFold model)
Mu-diguetoxin-Dc1aBprotein57Diguetia canitiesP49126 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6A95_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
>6A95_2 Mu-diguetoxin-Dc1a (chains B)
SAKDGDVEGPAGCKKYDVECDSGECCQKQYLWYKWRPLDCRCLKSGFFSSKCVCRDV

Ligands and cofactors

IDNameFormulaCopies
9SR(1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diaz…C11 H17 N3 O81
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O63

Water and common crystallization additives (NA) are not listed.

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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