6NT4: Human-cockroach hybrid Nav channel

Cryo-EM structure of a human-cockroach hybrid Nav channel bound to alpha-scorpion toxin AaH2. Determined by electron microscopy at 3.5 Å resolution. Released 20 Feb 2019.

Method
Electron microscopy
Resolution
3.5 Å
Organisms
Periplaneta americana, Homo sapiens, Androctonus australis
Chains
3
Atoms
11,924
Mol. weight
201.45 kDa
Ligands
NAG, 76F, AJP, LHG
Released
20 Feb 2019

Explore 6NT4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NT4 contains 78 α-helices and 21 β-strands across 3 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: 75 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix541
α-helix55-595
β-strand7611
β-strand8111
α-helix100-10910
α-helix130-1378
α-helix140-15718
α-helix166-18722
α-helix192-1965
α-helix200-21415
α-helix228-23912
α-helix245-27531
β-strand287-29042
α-helix305-3106
α-helix337-3382
β-strand341-34442
α-helix352-3543
α-helix361-37212
α-helix377-38812
α-helix390-3923
α-helix393-4019
α-helix404-4085
α-helix409-43224
α-helix503-51614
α-helix522-53615
α-helix545-57228
α-helix578-5814
α-helix584-60320
α-helix609-6135
α-helix614-6229
α-helix625-63612
α-helix639-66224
α-helix666-6694
α-helix687-69913
α-helix703-7119
α-helix718-72710
α-helix728-7325
α-helix733-7408
α-helix839-85214
α-helix856-87015
α-helix871-8733
α-helix886-91227
α-helix914-9174
α-helix923-94220
α-helix945-9462
α-helix948-9503
α-helix955-9584
α-helix959-9624
α-helix966-9683
α-helix969-100335
β-strand101013
β-strand101214
β-strand101814
α-helix1027-10326
β-strand103813
α-helix1039-10402
α-helix1048-105811
α-helix1064-10729
α-helix1089-110012
α-helix1104-11074
α-helix1109-112315
α-helix1133-11408
α-helix1141-11444
α-helix1160-11645
α-helix1170-11734
α-helix1177-11859
α-helix1186-11894
α-helix1198-122326
α-helix1232-124615
α-helix1261-127212
α-helix1274-12774
α-helix1291-12944
α-helix1296-132025
α-helix1340-134910
α-helix1355-13628
β-strand137215
β-strand137715
α-helix1385-13895
α-helix1394-13974
α-helix1398-14025
α-helix1403-142321
α-helix1427-143913
β-strand144716
α-helix1451-14566
α-helix1473-14764
β-strand148816
α-helix1489-150315
Chain B: 2 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix19-279
β-strand34-3747
β-strand45-4847
α-helix56-572
Chain C: 1 helix, 7 β-strands
ElementResiduesLengthSheet
β-strand2-438
β-strand619
β-strand7110
β-strand13110
α-helix20-278
β-strand33-3758
β-strand45-5178
β-strand5719

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha,Sodium channel protein…Aprotein1559Periplaneta americana, Homo sapiensD0E0C2 (AlphaFold model), Q15858 (AlphaFold model)
Alpha-mammal toxin AaH2B, Cprotein65Androctonus australisP01484 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6NT4_1 Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha,Sodium channel protein PaFPC1 (chains A)
WSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSGGDYKDDDDKGGSGGDYKDDDDKMADNSP
LIREERQRLFRPYTRAMLTAPSAQPAKENGKTEENKDNSRDKGRGANKDRDGSAHPDQAL
EQGSRLPARMRNIFPAELASTPLEDFDPFYKNKKTFVVVTKAGDIFRFSGEKSLWMLDPF
TPIRRVAISTMVQPIFSYFIMITILIHCIFMIMPATQTTYILELVFLSIYTIEVVVKVLA
RGFILHPFAYLRDPWNWLDFLVTLIGYITLVVDLGHLYALRAFRVLRSWRTVTIVPGWRT
IVDALSLSITSLKDLVLLLLFSLSVFALIGLQLFMGNLKHKCVKHFPADGSWGNFTDERW
FNYTSNSSHWYIPDDWIEYPLCGNSSGAGMCPPGYTCLQGYGGNPNYGYTSFDTFGWAFL
SVFRLVTLDYWEDLYQLALRSAGPWHILFFIIVVFYGTFCFLNFILAVVVMSYTHMVKRA
DEEKAAERELKKEKKAASVANNTANGQEQTTIEMNGDEAVVIDNNDQAARQQSDPETPAP
SVTQRLTDFLCVWDCCVPWQKLQGAIGAVVLSPFFELFIAVIIVLNITFMALDHHDMNIE
FERILRTGNYIFTSIYIVEAVLKIIALSPKFYFKDSWNVFDFIIVVFAILELGLEGVQGL
SVFRSFRLLRVFRLAKFWPTLNNFMSVMTKSYGAFVNVMYVMFLLLFIFAIIGMQLFGMN
YIDNMERFPDGDLPRWNFTDFLHSFMIVFRALCGEWIESMWDCMLVGDWSCIPFFVAVFF
VGNLVILNLLIALLLNNYGSFCTSPTSDEEDSKDEDALAQIVRIFKRFKPNLNAVKLSPM
KPDSEDIVESQEIQGNNIADAEDVLAGEFPPDCCCNAFYKCFPSRPARDSSVQRMWSNIR
RVCFLLAKNKYFQKFVTAVLVITSVLLALEDIYLPQRPVLVNITLYVDYVLTAFFVIEMI
IMLFAVGFKKYFTSKWYWLDFIVVVAYLLNFVLMCAGIEALQTLRLLRVFRLFRPLSKVN
GMQVVTSTLVEAVPHIFNVILVGIFFWLVFAIMGVQLFAGKFYKCVDENSTVLSHEITMD
RNDCLHENYTWENSPMNFDHVGNAYLSLLQVATFKGWLQIMNDAIDSREVHKQPIRETNI
YMYLYFIFFIVFGSFFILKLFVCILIDIFRQQRRKAEGLSATDSRTQLIYRRAVMRTMSA
KPVKRIPKPGNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTEVLYWIN
VVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFRV
IRLARIGRILRLVKGAKGIRLLLLALRKALRTLFNVSFLLFVIMFVYAVFGMEFFMHIRD
AGAIDDVYNFKTFGQSIILLFQLATSAGWDGVYFAIANEEDCRAPDHELGYPGNCGSRAL
GIAYLVSYLIITCLVVINMYAAVILDYVLEVYEDSKEGLTDDDYDMFFEVWQQFDPEATQ
YIRYDQLSELLEALQPPLQVQKPNKYKILSMNIPICKDDHIFYKDVLEALVKDVFSRRG
Sequence of entity 2 (B, C), FASTA
>6NT4_2 Alpha-mammal toxin AaH2 (chains B, C)
VKDGYIVDDVNCTYFCGRNAYCNEECTKLKGESGYCQWASPYGNACYCYKLPDHVRTKGP
GRCHX

Ligands and cofactors

IDNameFormulaCopies
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O65
76F(7E,21R,24S)-27-amino-24-hydroxy-18,24-dioxo-19,23,25-trioxa-24lambda~5~-phosph…C41 H76 N O8 P5
AJPDigitoninC56 H92 O291
LHG1,2-dipalmitoyl-phosphatidyl-glyceroleC38 H75 O10 P1
Y01Cholesterol hemisuccinateC31 H50 O41

Primary citation

Structural basis of alpha-scorpion toxin action on Na v channels. Clairfeuille, T., Cloake, A., Infield, D.T. et al. Science (2019) 363. DOI 10.1126/science.aav8573 · 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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