9DK5: Human Nav1.6
Cryo-EM structure of human Nav1.6 in complex with PaurTx3. Determined by electron microscopy at 2.9 Å resolution. Released 17 Sept 2025.
- Method
- Electron microscopy
- Resolution
- 2.9 Å
- Organisms
- Homo sapiens, Paraphysa scrofa
- Chains
- 5
- Atoms
- 12,873
- Mol. weight
- 273.51 kDa
- Ligands
- NAG, Y01, PCW, CLR
- Released
- 17 Sept 2025
Explore 9DK5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9DK5 contains 79 α-helices and 54 β-strands across 5 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, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 19-34 | 16 | |
| β-strand | 64 | 1 | 1 |
| α-helix | 65-66 | 2 | |
| α-helix | 67-69 | 3 | |
| α-helix | 72-73 | 2 | |
| β-strand | 80-81 | 2 | 2 |
| β-strand | 93-97 | 5 | 2 |
| β-strand | 102 | 1 | 1 |
| β-strand | 103-107 | 5 | 2 |
| α-helix | 110 | 1 | |
| β-strand | 111 | 1 | 3 |
| β-strand | 115 | 1 | 3 |
| α-helix | 120-129 | 10 | |
| α-helix | 132-148 | 17 | |
| α-helix | 158-179 | 22 | |
| α-helix | 189-191 | 3 | |
| α-helix | 193-211 | 19 | |
| α-helix | 216-219 | 4 | |
| α-helix | 220-224 | 5 | |
| α-helix | 225-233 | 9 | |
| α-helix | 237-246 | 10 | |
| α-helix | 248-250 | 3 | |
| α-helix | 252-272 | 21 | |
| α-helix | 276-278 | 3 | |
| β-strand | 279-283 | 5 | 4 |
| β-strand | 293 | 1 | 5 |
| β-strand | 296 | 1 | 5 |
| α-helix | 302-305 | 4 | |
| α-helix | 309-311 | 3 | |
| β-strand | 312 | 1 | 4 |
| α-helix | 321-323 | 3 | |
| α-helix | 333-334 | 2 | |
| β-strand | 337-341 | 5 | 4 |
| α-helix | 347-349 | 3 | |
| β-strand | 355 | 1 | 6 |
| α-helix | 356-368 | 13 | |
| α-helix | 372-383 | 12 | |
| α-helix | 385-387 | 3 | |
| α-helix | 388-413 | 26 | |
| α-helix | 738-749 | 12 | |
| α-helix | 753-770 | 18 | |
| α-helix | 779-806 | 28 | |
| α-helix | 816-833 | 18 | |
| β-strand | 834 | 1 | 7 |
| α-helix | 835-838 | 4 | |
| α-helix | 841-856 | 16 | |
| α-helix | 859-872 | 14 | |
| α-helix | 876-897 | 22 | |
| α-helix | 900-903 | 4 | |
| α-helix | 905-908 | 4 | |
| α-helix | 922-933 | 12 | |
| α-helix | 938-948 | 11 | |
| α-helix | 950-979 | 30 | |
| α-helix | 997-1006 | 10 | |
| α-helix | 1179-1196 | 18 | |
| α-helix | 1198-1213 | 16 | |
| α-helix | 1214-1217 | 4 | |
| α-helix | 1222-1225 | 4 | |
| α-helix | 1226-1254 | 29 | |
| α-helix | 1256-1259 | 4 | |
| α-helix | 1263-1284 | 22 | |
| α-helix | 1290-1296 | 7 | |
| α-helix | 1297-1306 | 10 | |
| α-helix | 1311-1322 | 12 | |
| α-helix | 1324-1349 | 26 | |
| β-strand | 1354-1358 | 5 | 8 |
| β-strand | 1363-1364 | 2 | 8 |
| α-helix | 1365-1366 | 2 | |
| β-strand | 1372 | 1 | 9 |
| α-helix | 1373-1379 | 7 | |
| β-strand | 1387-1391 | 5 | 8 |
| α-helix | 1399-1410 | 12 | |
| α-helix | 1415-1424 | 10 | |
| β-strand | 1430 | 1 | 9 |
| α-helix | 1438-1440 | 3 | |
| α-helix | 1441-1447 | 7 | |
| α-helix | 1448-1454 | 7 | |
| α-helix | 1455-1474 | 20 | |
| α-helix | 1483-1495 | 13 | |
| α-helix | 1510-1519 | 10 | |
| α-helix | 1522-1540 | 19 | |
| β-strand | 1543 | 1 | 6 |
| α-helix | 1548-1575 | 28 | |
| α-helix | 1580-1582 | 3 | |
| α-helix | 1584-1606 | 23 | |
| α-helix | 1613-1620 | 8 | |
| α-helix | 1621-1623 | 3 | |
| α-helix | 1624-1627 | 4 | |
| α-helix | 1630-1633 | 4 | |
| α-helix | 1635-1672 | 38 | |
| α-helix | 1691-1702 | 12 | |
| α-helix | 1707-1714 | 8 | |
| β-strand | 1726 | 1 | 10 |
| β-strand | 1733 | 1 | 10 |
| α-helix | 1739-1771 | 33 | |
Chain C: 3 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-27 | 3 | |
| β-strand | 29-31 | 3 | 11 |
| β-strand | 36-38 | 3 | 12 |
| β-strand | 41 | 1 | 13 |
| β-strand | 51-61 | 11 | 14 |
| β-strand | 68-74 | 7 | 14 |
| β-strand | 77-80 | 4 | 14 |
| β-strand | 90-92 | 3 | 12 |
| β-strand | 103 | 1 | 13 |
| β-strand | 106-108 | 3 | 12 |
| α-helix | 113-115 | 3 | |
| β-strand | 117-129 | 13 | 14 |
| β-strand | 132-135 | 4 | 14 |
| β-strand | 138-144 | 7 | 14 |
| β-strand | 145-147 | 3 | 11 |
| α-helix | 154-191 | 38 | |
Chain H: 0 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 8 | 1 | 15 |
| β-strand | 10 | 1 | 16 |
| β-strand | 13 | 1 | 16 |
| β-strand | 22-23 | 2 | 17 |
| β-strand | 29 | 1 | 15 |
| β-strand | 30-31 | 2 | 17 |
| β-strand | 32 | 1 | 7 |
Chain I: 1 helix, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 18 |
| β-strand | 8 | 1 | 19 |
| β-strand | 16 | 1 | 18 |
| α-helix | 17 | 1 | |
| β-strand | 21-22 | 2 | 20 |
| β-strand | 29 | 1 | 19 |
| β-strand | 31-32 | 2 | 20 |
Chain J: 2 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 21 |
| β-strand | 8 | 1 | 22 |
| β-strand | 16 | 1 | 21 |
| β-strand | 21 | 1 | 23 |
| β-strand | 29 | 1 | 22 |
| α-helix | 31 | 1 | |
| β-strand | 32 | 1 | 23 |
| α-helix | 33 | 1 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Sodium channel protein type 8 subunit alpha | A | protein | 1980 | Homo sapiens | Q9UQD0 (AlphaFold model) |
| Sodium channel subunit beta-1 | C | protein | 218 | Homo sapiens | Q07699 (AlphaFold model) |
| Beta-theraphotoxin-Ps1a | H, I, J | protein | 34 | Paraphysa scrofa | P84510 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>9DK5_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
>9DK5_2 Sodium channel subunit beta-1 (chains C)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE
Sequence of entity 3 (H, I, J), FASTA
>9DK5_3 Beta-theraphotoxin-Ps1a (chains H, I, J)
DCLGFLWKCNPSNDKCCRPNLVCSRKDKWCKYQI
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 7 |
| Y01 | Cholesterol hemisuccinate | C31 H50 O4 | 3 |
| PCW | 1,2-dioleoyl-sn-glycero-3-phosphocholine | C44 H85 N O8 P | 4 |
| CLR | Cholesterol | C27 H46 O | 1 |
| P5S | O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine | C42 H82 N O10 P | 1 |
| 9Z9 | (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en | C34 H56 O5 | 1 |
| P3X | (5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosph… | C35 H68 N O8 P | 1 |
| LPE | 1-O-octadecyl-sn-glycero-3-phosphocholine | C26 H57 N O6 P | 1 |
Primary citation
Diverse modulation mechanisms of human Nav1.6 by gating modifier neurotoxins. Fan, X., Jian, H., Chen, J. et al. To be published.
Other PDB entries of the same protein (UniProt Q9UQD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 25II 2.5 Å, Cryo-EM structure of human Nav1.6 in complex with Iota-Conotoxin RXIA
- 25IH 2.8 Å, Cryo-EM structure of human Nav1.6 in complex with Cn2
- 25IJ 3.1 Å, Cryo-EM structure of human Nav1.6 in complex with delta-paraponeritoxin-Pc1a
- 8FHD 3.1 Å, Cryo-EM structure of human voltage-gated sodium channel Nav1.6
- 8GZ2 3.3 Å, Cryo-EM structure of human NaV1.6/beta1/beta2-4,9-anhydro-tetrodotoxin
- 8GZ1 3.4 Å, Cryo-EM structure of human NaV1.6/beta1/beta2,apo state
Browse structure collections
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