25IJ: Human Nav1.6

Cryo-EM structure of human Nav1.6 in complex with delta-paraponeritoxin-Pc1a. Determined by electron microscopy at 3.1 Å resolution. Released 20 May 2026.

Method
Electron microscopy
Resolution
3.1 Å
Organisms
Homo sapiens, Paraponera clavata
Chains
3
Atoms
12,227
Mol. weight
255.23 kDa
Ligands
Y01, PCW, 9Z9, NAG
Released
20 May 2026

Explore 25IJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

25IJ contains 90 α-helices and 33 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: 85 helices, 21 β-strands

ElementResiduesLengthSheet
α-helix19-2810
α-helix29-335
α-helix57-593
β-strand6411
α-helix65-662
α-helix67-693
α-helix72-732
β-strand8112
α-helix86-883
β-strand93-9752
β-strand10211
β-strand103-10752
α-helix120-1289
α-helix132-14817
α-helix156-1583
α-helix160-17920
α-helix181-1822
α-helix189-1913
α-helix193-21018
α-helix219-2224
α-helix223-2286
α-helix229-2335
α-helix237-24610
α-helix249-2513
α-helix252-27221
α-helix276-2783
β-strand279-28353
α-helix288-2903
β-strand29214
β-strand29814
α-helix302-3065
α-helix309-3113
β-strand31213
α-helix321-3233
α-helix333-3342
β-strand337-34153
α-helix344-3452
α-helix356-36813
α-helix372-38312
α-helix385-3873
α-helix388-39912
α-helix403-42624
α-helix738-75013
α-helix753-77018
β-strand77415
α-helix779-80527
α-helix809-8124
α-helix816-83318
α-helix835-8373
α-helix840-8467
α-helix847-85711
α-helix859-87214
α-helix876-89722
α-helix900-9034
α-helix905-9084
α-helix922-93312
α-helix938-94811
α-helix950-98132
α-helix997-10059
α-helix1179-119618
α-helix1198-121316
α-helix1214-12174
α-helix1220-12234
α-helix1226-125429
α-helix1256-12594
α-helix1263-128422
α-helix1290-12956
α-helix1297-130711
α-helix1311-132212
α-helix1324-134926
β-strand1354-135856
β-strand1363-136426
α-helix1365-13662
β-strand137217
α-helix1373-13808
β-strand1387-139156
β-strand139815
α-helix1399-141012
α-helix1415-14239
β-strand143017
α-helix1431-14322
α-helix1438-14403
α-helix1441-14477
α-helix1448-14536
α-helix1454-147421
α-helix1483-149715
α-helix1503-15064
α-helix1512-15209
α-helix1522-154019
α-helix1548-157629
α-helix1579-15824
α-helix1586-160217
α-helix1605-16073
α-helix1613-16197
α-helix1622-16254
α-helix1626-16327
α-helix1636-164611
α-helix1648-167225
β-strand167918
β-strand168218
α-helix1691-170212
α-helix1707-17115
α-helix1712-17154
β-strand172619
β-strand173319
α-helix1739-177133
Chain B: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix2-1110
α-helix13-2412
Chain C: 3 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix25-273
β-strand29-31310
β-strand36-38311
β-strand41112
β-strand50-611213
β-strand68-74713
β-strand77-80413
β-strand90-92311
β-strand103112
β-strand106-108311
α-helix113-1153
β-strand117-1291313
β-strand132-1441313
β-strand145-147310
α-helix154-19138

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein type 8 subunit alphaAprotein1980Homo sapiensQ9UQD0 (AlphaFold model)
Delta-paraponeritoxin-Pc1aBprotein26Paraponera clavataP41736 (AlphaFold model)
Sodium channel regulatory subunit beta-1Cprotein173Homo sapiensQ07699 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>25IJ_1 Sodium channel protein type 8 subunit alpha (chains A)
MAARLLAPPGPDSFKPFTPESLANIERRIAESKLKKPPKADGSHREDDEDSKPKPNSDLE
AGKSLPFIYGDIPQGLVAVPLEDFDPYYLTQKTFVVLNRGKTLFRFSATPALYILSPFNL
IRRIAIKILIHSVFSMIIMCTILTNCVFMTFSNPPDWSKNVEYTFTGIYTFESLVKIIAR
GFCIDGFTFLRDPWNWLDFSVIMMAYITEFVNLGNVSALRTFRVLRALKTISVIPGLKTI
VGALIQSVKKLSDVMILTVFCLSVFALIGLQLFMGNLRNKCVVWPINFNESYLENGTKGF
DWEEYINNKTNFYTVPGMLEPLLCGNSSDAGQCPEGYQCMKAGRNPNYGYTSFDTFSWAF
LALFRLMTQDYWENLYQLTLRAAGKTYMIFFVLVIFVGSFYLVNLILAVVAMAYEEQNQA
TLEEAEQKEAEFKAMLEQLKKQQEEAQAAAMATSAGTVSEDAIEEEGEEGGGSPRSSSEI
SKLSSKSAKERRNRRKKRKQKELSEGEEKGDPEKVFKSESEDGMRRKAFRLPDNRIGRKF
SIMNQSLLSIPGSPFLSRHNSKSSIFSFRGPGRFRDPGSENEFADDEHSTVEESEGRRDS
LFIPIRARERRSSYSGYSGYSQGSRSSRIFPSLRRSVKRNSTVDCNGVVSLIGGPGSHIG
GRLLPEATTEVEIKKKGPGSLLVSMDQLASYGRKDRINSIMSVVTNTLVEELEESQRKCP
PCWYKFANTFLIWECHPYWIKLKEIVNLIVMDPFVDLAITICIVLNTLFMAMEHHPMTPQ
FEHVLAVGNLVFTGIFTAEMFLKLIAMDPYYYFQEGWNIFDGFIVSLSLMELSLADVEGL
SVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKS
YKECVCKINQDCELPRWHMHDFFHSFLIVFRVLCGEWIETMWDCMEVAGQAMCLIVFMMV
MVIGNLVVLNLFLALLLSSFSADNLAATDDDGEMNNLQISVIRIKKGVAWTKLKVHAFMQ
AHFKQREADEVKPLDELYEKKANCIANHTGADIHRNGDFQKNGNGTTSGIGSSVEKYIID
EDHMSFINNPNLTVRVPIAVGESDFENLNTEDVSSESDPEGSKDKLDDTSSSEGSTIDIK
PEVEEVPVEQPEEYLDPDACFTEGCVQRFKCCQVNIEEGLGKSWWILRKTCFLIVEHNWF
ETFIIFMILLSSGALAFEDIYIEQRKTIRTILEYADKVFTYIFILEMLLKWTAYGFVKFF
TNAWCWLDFLIVAVSLVSLIANALGYSELGAIKSLRTLRALRPLRALSRFEGMRVVVNAL
VGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGKYHYCFNETSEIRFEIEDVNNKTECEKLM
EGNNTEIRWKNVKINFDNVGAGYLALLQVATFKGWMDIMYAAVDSRKPDEQPKYEDNIYM
YIYFVIFIIFGSFFTLNLFIGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKLGSKKP
QKPIPRPLNKIQGIVFDFVTQQAFDIVIMMLICLNMVTMMVETDTQSKQMENILYWINLV
FVIFFTCECVLKMFALRHYYFTIGWNIFDFVVVILSIVGMFLADIIEKYFVSPTLFRVIR
LARIGRILRLIKGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIFSIFGMSNFAYVKHEA
GIDDMFNFETFGNSMICLFQITTSAGWDGLLLPILNRPPDCSLDKEHPGSGFKGDCGNPS
VGIFFFVSYIIISFLIVVNMYIAIILENFSVATEESADPLSEDDFETFYEIWEKFDPDAT
QFIEYCKLADFADALEHPLRVPKPNTIELIAMDLPMVSGDRIHCLDILFAFTKRVLGDSG
ELDILRQQMEERFVASNPSKVSYEPITTTLRRKQEEVSAVVLQRAYRGHLARRGFICKKT
TSNKLENGGTHREKKESTPSTASLPSYDSVTKPEKEKQQRAEEGRRERAKRQKEVRESKC
Sequence of entity 2 (B), FASTA
>25IJ_2 Delta-paraponeritoxin-Pc1a (chains B)
FLPLLILGSLLMTPPVIQAIHDAQRX
Sequence of entity 3 (C), FASTA
>25IJ_3 Sodium channel regulatory subunit beta-1 (chains C)
GCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFRQKGTEEFVKILRYENEVLQ
LEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYECHVYRLLFFENYEHNTSVV
KKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIYCYKKIAAATETA

Ligands and cofactors

IDNameFormulaCopies
Y01Cholesterol hemisuccinateC31 H50 O42
PCW1,2-dioleoyl-sn-glycero-3-phosphocholineC44 H85 N O8 P3
9Z9(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-enC34 H56 O51
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O64

Primary citation

Diverse binding poses of agonistic neurotoxins on human Na v 1.6. Fan, X., Huang, J., Yang, L. et al. Nature (2026) 656:250-259. DOI 10.1038/s41586-026-10661-x · PubMed

Other PDB entries of the same protein (UniProt Q9UQD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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