8GZ1: Human NaV1.6/beta1/beta2,apo state

Cryo-EM structure of human NaV1.6/beta1/beta2,apo state. Determined by electron microscopy at 3.4 Å resolution. Released 8 Mar 2023.

Method
Electron microscopy
Resolution
3.4 Å
Organism
Homo sapiens
Chains
3
Atoms
11,912
Mol. weight
278.03 kDa
Ligands
NAG
Released
8 Mar 2023

Explore 8GZ1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GZ1 contains 69 α-helices and 34 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 B: 66 helices, 12 β-strands

ElementResiduesLengthSheet
α-helix132-15019
α-helix156-1583
α-helix159-17820
α-helix189-1913
α-helix193-20816
α-helix216-2216
α-helix224-23310
α-helix237-25014
α-helix252-27221
α-helix276-2783
β-strand27914
β-strand28015
β-strand28316
α-helix288-2903
α-helix302-3054
α-helix309-3113
α-helix321-3222
β-strand32315
β-strand33716
β-strand34114
α-helix344-3452
α-helix347-3493
α-helix356-36813
α-helix372-38312
α-helix385-3873
α-helix388-3947
α-helix395-3995
α-helix401-42525
α-helix722-7309
α-helix737-75014
α-helix752-7543
α-helix756-77116
α-helix779-80628
α-helix809-8135
α-helix816-83318
α-helix844-85613
α-helix859-87214
α-helix876-90328
α-helix905-9084
α-helix922-93413
α-helix938-94811
α-helix950-98031
α-helix1184-119613
α-helix1198-121316
α-helix1226-125429
α-helix1256-12605
α-helix1263-128321
α-helix1290-12967
α-helix1297-13048
α-helix1305-13095
α-helix1311-132313
α-helix1325-134925
β-strand135417
β-strand1357-135828
α-helix1364-13663
β-strand137219
α-helix1373-138210
β-strand1387-138828
β-strand139117
α-helix1399-141012
α-helix1415-14239
β-strand143019
α-helix1438-14403
α-helix1441-14499
α-helix1450-14545
α-helix1455-147319
α-helix1483-149513
α-helix1505-15073
α-helix1510-152011
α-helix1522-154019
α-helix1548-158033
α-helix1584-160421
α-helix1613-16219
α-helix1622-163312
α-helix1636-167338
α-helix1691-170212
α-helix1707-17115
α-helix1739-177133
Chain C: 1 helix, 12 β-strands
ElementResiduesLengthSheet
β-strand32-33210
β-strand38-40311
β-strand46-48312
β-strand51-52210
β-strand64-70711
β-strand77-84811
β-strand87-89311
β-strand99-100212
β-strand112-114312
α-helix119-1213
β-strand123-130811
β-strand137-138211
β-strand141-146611
Chain D: 2 helices, 10 β-strands
ElementResiduesLengthSheet
α-helix25-273
β-strand29-3131
β-strand36-4052
β-strand50-60113
β-strand68-7363
β-strand78-8033
β-strand90-9232
β-strand104-10852
β-strand117-128123
β-strand134-144113
β-strand145-14731
α-helix154-18936

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Sodium channel subunit beta-1Dprotein218Homo sapiensQ07699 (AlphaFold model)
Sodium channel protein type 8 subunit alphaBprotein1980Homo sapiensQ9UQD0 (AlphaFold model)
Sodium channel subunit beta-2Cprotein215Homo sapiensO60939 (AlphaFold model)
Sequence of entity 1 (D), FASTA
>8GZ1_1 Sodium channel subunit beta-1 (chains D)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE
Sequence of entity 2 (B), FASTA
>8GZ1_2 Sodium channel protein type 8 subunit alpha (chains B)
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 3 (C), FASTA
>8GZ1_3 Sodium channel subunit beta-2 (chains C)
MHRDAWLPRPAFSLTGLSLFFSLVPPGRSMEVTVPATLNVLNGSDARLPCTFNSCYTVNH
KQFSLNWTYQECNNCSEEMFLQFRMKIINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPE
DEGIYNCYIMNPPDRHRGHGKIHLQVLMEEPPERDSTVAVIVGASVGGFLAVVILVLMVV
KCVRRKKEQKLSTDDLKTEEEGKTDGEGNPDDGAK

Ligands and cofactors

IDNameFormulaCopies
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O62

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

Primary citation

Structure of human Na V 1.6 channel reveals Na + selectivity and pore blockade by 4,9-anhydro-tetrodotoxin. Li, Y., Yuan, T., Huang, B. et al. Nat Commun (2023) 14:1030-1030. DOI 10.1038/s41467-023-36766-9 · PubMed

Other PDB entries of the same protein (UniProt Q07699 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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