6A90: Sodium channel protein PaFPC1

Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and Dc1a. Determined by electron microscopy at 2.8 Å resolution. Released 8 Aug 2018.

Method
Electron microscopy
Resolution
2.8 Å
Organisms
Periplaneta americana, Diguetia canities
Chains
2
Atoms
11,085
Mol. weight
191.91 kDa
Ligands
NAG
Released
8 Aug 2018

Explore 6A90 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6A90 contains 85 α-helices and 23 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: 84 helices, 15 β-strands

ElementResiduesLengthSheet
α-helix53-553
α-helix56-605
α-helix98-10912
α-helix130-1378
α-helix142-15817
α-helix160-1612
α-helix163-18220
α-helix196-1983
α-helix204-21613
α-helix226-23510
α-helix238-2403
α-helix244-25714
α-helix259-27921
α-helix283-2853
β-strand287-29041
α-helix291-2933
α-helix305-3117
α-helix313-3153
β-strand31611
α-helix325-3273
α-helix337-3382
β-strand341-34441
α-helix361-37313
α-helix377-3859
α-helix390-3923
α-helix393-3997
α-helix400-4078
α-helix408-43427
α-helix503-51614
α-helix521-53717
β-strand543-54422
α-helix545-57026
α-helix575-5784
α-helix582-59918
α-helix609-61911
α-helix620-6234
α-helix625-63612
α-helix639-66224
α-helix666-6694
α-helix671-6733
α-helix687-69812
α-helix703-7119
α-helix717-7259
α-helix726-7327
α-helix733-7353
α-helix737-7437
α-helix836-85318
α-helix856-87116
α-helix873-8753
α-helix884-91734
α-helix921-94121
α-helix944-9474
α-helix948-9514
α-helix952-9587
α-helix959-9624
α-helix968-97710
α-helix979-100426
β-strand1009-101243
β-strand101813
α-helix1019-10202
β-strand102614
α-helix1027-10326
β-strand1036-103943
α-helix1047-105812
α-helix1063-107210
β-strand107814
α-helix1086-10883
α-helix1089-10957
α-helix1096-11005
α-helix1105-112218
α-helix1133-11419
α-helix1148-11558
α-helix1162-11654
α-helix1170-118516
α-helix1186-11894
α-helix1198-122326
α-helix1228-12303
α-helix1232-124817
α-helix1261-12699
α-helix1270-12778
α-helix1283-132139
β-strand132715
β-strand133015
α-helix1339-134810
α-helix1349-13513
α-helix1355-13628
β-strand137216
β-strand137716
α-helix1384-139411
α-helix1395-14028
α-helix1404-142219
α-helix1427-143711
β-strand1447-144937
α-helix1451-14599
α-helix14611
α-helix1471-14777
β-strand1486-148837
α-helix1489-150416
α-helix1509-151911
Chain B: 1 helix, 8 β-strands
ElementResiduesLengthSheet
β-strand7-828
β-strand1419
β-strand1912
β-strand2519
β-strand28-3038
β-strand35-3628
α-helix371
β-strand38-4472
β-strand50-5672

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein PaFPC1Aprotein1596Periplaneta americanaD0E0C2 (AlphaFold model)
Mu-diguetoxin-Dc1aBprotein57Diguetia canitiesP49126 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6A90_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
>6A90_2 Mu-diguetoxin-Dc1a (chains B)
SAKDGDVEGPAGCKKYDVECDSGECCQKQYLWYKWRPLDCRCLKSGFFSSKCVCRDV

Ligands and cofactors

IDNameFormulaCopies
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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