8FHD: Human voltage-gated sodium channel Nav1.6

Cryo-EM structure of human voltage-gated sodium channel Nav1.6. Determined by electron microscopy at 3.1 Å resolution. Released 8 Feb 2023.

Method
Electron microscopy
Resolution
3.1 Å
Organism
Homo sapiens
Chains
2
Atoms
12,686
Mol. weight
263.82 kDa
Ligands
LPE, PCW, CLR, Y01
Released
8 Feb 2023

Explore 8FHD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FHD contains 69 α-helices and 25 β-strands across 2 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: 67 helices, 13 β-strands

ElementResiduesLengthSheet
α-helix19-3416
α-helix64-663
α-helix67-693
β-strand8111
β-strand94-9741
β-strand103-10641
α-helix1101
β-strand11112
β-strand11512
α-helix117-1193
α-helix122-1298
α-helix132-15019
α-helix156-1583
α-helix159-17921
β-strand18213
β-strand18913
α-helix193-20715
α-helix216-2238
α-helix224-2285
α-helix229-2335
α-helix237-24913
α-helix253-27220
β-strand279-28354
α-helix288-2903
α-helix321-3222
β-strand32314
β-strand337-34154
α-helix356-36712
α-helix372-38312
α-helix385-3873
α-helix388-3969
α-helix401-44343
α-helix739-7479
α-helix753-77018
α-helix779-80628
α-helix820-83213
α-helix840-8434
α-helix847-85610
α-helix859-87113
α-helix876-89722
α-helix900-9034
α-helix905-9073
α-helix922-93413
α-helix938-94811
α-helix951-97929
α-helix981-9833
α-helix996-100611
α-helix1179-119618
α-helix1200-121415
α-helix1220-12234
α-helix1226-125429
α-helix1256-12605
α-helix1263-128422
α-helix1290-12967
α-helix1297-13015
α-helix1311-134636
β-strand1354-135855
β-strand1363-136425
α-helix1365-13662
α-helix1373-13797
β-strand1387-139155
α-helix1399-141012
α-helix1415-142410
α-helix1438-14403
α-helix1441-14499
α-helix1450-14545
α-helix1455-147420
α-helix1483-149614
α-helix1498-15003
α-helix1514-15196
α-helix1522-153817
α-helix1548-157225
α-helix1585-159713
α-helix1598-16025
α-helix1603-16053
α-helix1615-16206
α-helix1621-163111
α-helix1635-167238
α-helix1691-170212
α-helix1739-177234
Chain C: 2 helices, 12 β-strands
ElementResiduesLengthSheet
β-strand29-3136
β-strand3817
β-strand4118
β-strand51-61119
β-strand68-7479
β-strand77-8049
β-strand91-9227
β-strand10318
β-strand106-10727
β-strand117-129139
β-strand132-143129
β-strand145-14736
α-helix150-1534
α-helix154-19138

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel protein type 8 subunit alphaAprotein1980Homo sapiensQ9UQD0 (AlphaFold model)
Sodium channel subunit beta-1Cprotein218Homo sapiensQ07699 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>8FHD_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
>8FHD_2 Sodium channel subunit beta-1 (chains C)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE

Ligands and cofactors

IDNameFormulaCopies
LPE1-O-octadecyl-sn-glycero-3-phosphocholineC26 H57 N O6 P5
PCW1,2-dioleoyl-sn-glycero-3-phosphocholineC44 H85 N O8 P3
CLRCholesterolC27 H46 O1
Y01Cholesterol hemisuccinateC31 H50 O44
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O67
P3X(5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosph…C35 H68 N O8 P1
9Z9(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-enC34 H56 O51
P5SO-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serineC42 H82 N O10 P2

Primary citation

Cryo-EM structure of human voltage-gated sodium channel Na v 1.6. Fan, X., Huang, J., Jin, X. et al. Proc Natl Acad Sci U S A (2023) 120:e2220578120-e2220578120. DOI 10.1073/pnas.2220578120 · 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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