25IH: Human Nav1.6

Cryo-EM structure of human Nav1.6 in complex with Cn2. Determined by electron microscopy at 2.8 Å resolution. Released 20 May 2026.

Method
Electron microscopy
Resolution
2.8 Å
Organisms
Homo sapiens, Centruroides noxius
Chains
3
Atoms
12,745
Mol. weight
272.07 kDa
Ligands
PCW, 9Z9, NAG, PT5
Released
20 May 2026

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

Secondary structure: helices and β-sheets

25IH contains 82 α-helices and 43 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: 76 helices, 20 β-strands

ElementResiduesLengthSheet
α-helix151
β-strand1611
α-helix171
α-helix19-3416
β-strand63-6421
α-helix65-662
α-helix67-693
α-helix72-732
β-strand80-8231
α-helix86-883
β-strand93-9751
β-strand102-10761
α-helix1101
β-strand11112
β-strand11512
α-helix120-13011
α-helix132-15019
α-helix156-1594
α-helix161-18020
α-helix189-1913
α-helix194-21118
α-helix217-2204
α-helix221-2299
α-helix230-2334
α-helix237-2459
α-helix249-2513
α-helix252-27221
α-helix276-2783
β-strand279-28353
α-helix288-2903
β-strand29214
β-strand29814
α-helix302-3054
α-helix309-3113
α-helix321-3233
α-helix333-3342
β-strand337-34153
α-helix344-3452
α-helix347-3493
α-helix356-36813
α-helix372-38312
α-helix385-3873
α-helix388-3947
α-helix395-4028
α-helix403-42927
α-helix739-75012
α-helix753-77119
β-strand77415
α-helix779-80628
α-helix809-8124
α-helix816-83318
α-helix834-8385
α-helix842-85615
α-helix859-87012
α-helix876-90328
α-helix905-9084
α-helix922-93413
α-helix937-94812
α-helix950-98132
α-helix1180-119617
α-helix1198-121316
α-helix1214-12174
α-helix1226-125429
α-helix1256-12594
α-helix1263-128422
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
β-strand139815
α-helix1399-141012
α-helix1415-142410
β-strand143017
α-helix1438-14403
α-helix1441-14477
α-helix1448-14547
α-helix1455-146915
α-helix1483-149614
α-helix1511-15199
α-helix1522-154019
α-helix1548-157225
α-helix1584-160623
α-helix1613-16208
α-helix1621-16299
α-helix1630-16334
α-helix1635-167238
α-helix1691-170212
β-strand172618
β-strand173318
α-helix1739-177032
Chain C: 3 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix25-273
β-strand29-3139
β-strand36-38310
β-strand41111
β-strand50-52312
β-strand55-61713
β-strand68-74713
β-strand77-80413
β-strand90-92310
β-strand103111
β-strand106-108310
α-helix113-1153
β-strand117-123713
β-strand126-129412
β-strand132-135412
β-strand138-144713
β-strand145-14739
α-helix154-19037
Chain D: 3 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand3-4214
β-strand6115
β-strand13115
β-strand15116
β-strand20114
α-helix23-3311
β-strand38-41414
β-strand45116
β-strand46-49414
α-helix601
α-helix63-653

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein type 8 subunit alphaAprotein1980Homo sapiensQ9UQD0 (AlphaFold model)
Sodium channel regulatory subunit beta-1Cprotein218Homo sapiensQ07699 (AlphaFold model)
Beta-mammal toxin Cn2Dprotein67Centruroides noxiusP01495 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>25IH_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
>25IH_2 Sodium channel regulatory subunit beta-1 (chains C)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE
Sequence of entity 3 (D), FASTA
>25IH_3 Beta-mammal toxin Cn2 (chains D)
KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPL
PNKRCSX

Ligands and cofactors

IDNameFormulaCopies
PCW1,2-dioleoyl-sn-glycero-3-phosphocholineC44 H85 N O8 P5
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 O66
PT5[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4…C47 H85 O19 P31
P3X(5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosph…C35 H68 N O8 P1
LPE1-O-octadecyl-sn-glycero-3-phosphocholineC26 H57 N O6 P1
P5SO-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serineC42 H82 N O10 P1
CLRCholesterolC27 H46 O1
Y01Cholesterol hemisuccinateC31 H50 O43

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

About this viewer

MolViewer shows 25IH directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.