25II: Human Nav1.6

Cryo-EM structure of human Nav1.6 in complex with Iota-Conotoxin RXIA. Determined by electron microscopy at 2.5 Å resolution. Released 20 May 2026.

Method
Electron microscopy
Resolution
2.5 Å
Organisms
Homo sapiens, Conus radiatus
Chains
3
Atoms
12,629
Mol. weight
267.09 kDa
Ligands
NAG, 9Z9, PCW, Y01
Released
20 May 2026

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

Secondary structure: helices and β-sheets

25II contains 78 α-helices and 37 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: 73 helices, 20 β-strands

ElementResiduesLengthSheet
β-strand1611
α-helix19-3416
β-strand6412
α-helix71-733
β-strand80-8231
β-strand93-9751
β-strand10212
β-strand103-10751
β-strand11213
β-strand11513
α-helix120-13011
α-helix132-14918
α-helix156-1583
α-helix159-17921
α-helix189-1913
α-helix193-21119
α-helix217-2226
α-helix223-2286
α-helix229-2335
α-helix237-24610
α-helix249-2513
α-helix252-27221
α-helix276-2783
β-strand279-28354
α-helix288-2903
β-strand29215
β-strand29815
α-helix302-3054
α-helix309-3113
β-strand31214
α-helix321-3233
α-helix333-3342
β-strand337-34154
α-helix356-36813
α-helix372-38312
α-helix385-3873
α-helix388-3947
α-helix395-4028
α-helix403-43533
α-helix739-75012
α-helix753-77018
α-helix779-80628
α-helix817-83216
α-helix840-8445
α-helix845-85612
α-helix859-87113
α-helix876-90328
α-helix905-9084
α-helix922-93413
α-helix938-94710
α-helix950-98031
α-helix997-100610
α-helix1180-119617
α-helix1198-121316
α-helix1214-12174
α-helix1220-12245
α-helix1226-125429
α-helix1256-12605
α-helix1263-128321
α-helix1286-12883
α-helix1290-12967
α-helix1297-13059
α-helix1306-13094
α-helix1311-134939
β-strand1354-135856
β-strand1363-136426
α-helix1365-13662
β-strand137217
α-helix1373-13808
β-strand1387-139156
α-helix1399-141113
α-helix1415-14228
β-strand143017
α-helix1438-14403
α-helix1441-14477
α-helix1448-14547
α-helix1455-146915
α-helix1483-149412
α-helix1514-15207
α-helix1522-153918
α-helix1548-157528
α-helix1585-160117
α-helix1603-16064
α-helix1613-16197
α-helix1620-163213
α-helix1635-164612
α-helix1648-167225
α-helix1691-170111
α-helix1707-17115
α-helix1713-17153
β-strand172618
β-strand173318
α-helix1739-177133
Chain C: 4 helices, 12 β-strands
ElementResiduesLengthSheet
α-helix25-273
β-strand29-3139
β-strand36-38310
β-strand41111
β-strand50-611212
β-strand68-74712
β-strand77-80412
α-helix84-863
β-strand90-92310
β-strand103111
β-strand106-108310
α-helix113-1153
β-strand117-1291312
β-strand132-1441312
β-strand145-14739
α-helix154-19037
Chain D: 1 helix, 5 β-strands
ElementResiduesLengthSheet
β-strand6113
β-strand11114
α-helix15-173
β-strand18113
β-strand21-23314
β-strand26-28314

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein type 8 subunit alphaAprotein1980Homo sapiensQ9UQD0 (AlphaFold model)
Sodium channel regulatory subunit beta-1Cprotein218Homo sapiensQ07699 (AlphaFold model)
Iota-conotoxin RXIADprotein46Conus radiatusQ7Z094 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>25II_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 (C), FASTA
>25II_2 Sodium channel regulatory subunit beta-1 (chains C)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE
Sequence of entity 3 (D), FASTA
>25II_3 Iota-conotoxin RXIA (chains D)
GPSFCKADEKPCEYHADCCNCCLSGICAPSTNWILPGCSTSSFFKI

Ligands and cofactors

IDNameFormulaCopies
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O67
9Z9(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-enC34 H56 O51
PCW1,2-dioleoyl-sn-glycero-3-phosphocholineC44 H85 N O8 P5
Y01Cholesterol hemisuccinateC31 H50 O43
CLRCholesterolC27 H46 O1
P5SO-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serineC42 H82 N O10 P1
LPE1-O-octadecyl-sn-glycero-3-phosphocholineC26 H57 N O6 P1
P3X(5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosph…C35 H68 N O8 P1

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

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:

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