8GZ2: Sodium channel subunit beta-1

Cryo-EM structure of human NaV1.6/beta1/beta2-4,9-anhydro-tetrodotoxin. Determined by electron microscopy at 3.3 Å resolution. Released 8 Mar 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 11,984
Mol. weight: 278.28 kDa
Ligands: WMK, NAG
Released: 8 Mar 2023

Explore 8GZ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GZ2 contains 70 α-helices and 39 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: 68 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	120-130	11
α-helix	132-150	19
α-helix	156-158	3
α-helix	159-178	20
α-helix	193-208	16
α-helix	216-221	6
α-helix	224-233	10
α-helix	237-250	14
α-helix	252-272	21
α-helix	276-278	3
β-strand	279	1	4
β-strand	280	1	5
β-strand	282-283	2	6
α-helix	288-290	3
α-helix	302-305	4
α-helix	309-311	3
β-strand	316	1	7
β-strand	318	1	7
α-helix	321-322	2
β-strand	323	1	5
β-strand	337-338	2	6
β-strand	341	1	4
α-helix	344-345	2
α-helix	347-349	3
α-helix	356-368	13
α-helix	372-383	12
α-helix	385-387	3
α-helix	388-394	7
α-helix	395-399	5
α-helix	400-423	24
α-helix	722-730	9
α-helix	737-749	13
α-helix	752-771	20
α-helix	779-806	28
α-helix	809-813	5
α-helix	816-833	18
α-helix	843-856	14
α-helix	860-872	13
α-helix	876-896	21
α-helix	900-903	4
α-helix	905-908	4
α-helix	922-934	13
α-helix	938-948	11
α-helix	950-959	10
α-helix	960-964	5
α-helix	965-980	16
α-helix	1184-1195	12
α-helix	1198-1213	16
α-helix	1226-1254	29
α-helix	1256-1260	5
α-helix	1263-1283	21
α-helix	1292-1296	5
α-helix	1297-1301	5
α-helix	1304-1309	6
α-helix	1311-1323	13
α-helix	1325-1349	25
β-strand	1354	1	8
β-strand	1357-1358	2	9
β-strand	1363-1364	2	9
β-strand	1372	1	10
α-helix	1373-1382	10
β-strand	1387	1	9
β-strand	1391	1	8
α-helix	1399-1411	13
α-helix	1415-1423	9
β-strand	1430	1	10
α-helix	1438-1440	3
α-helix	1441-1447	7
α-helix	1448-1454	7
α-helix	1455-1473	19
α-helix	1483-1495	13
α-helix	1505-1507	3
α-helix	1510-1520	11
α-helix	1522-1540	19
α-helix	1548-1580	33
α-helix	1584-1604	21
α-helix	1613-1621	9
α-helix	1622-1633	12
α-helix	1636-1672	37
α-helix	1691-1702	12
α-helix	1707-1711	5
α-helix	1718-1720	3
α-helix	1739-1771	33

Chain C: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	11
β-strand	37-40	4	12
β-strand	46-48	3	13
β-strand	51-52	2	11
β-strand	64-70	7	12
β-strand	77-84	8	12
β-strand	87-89	3	12
β-strand	99-101	3	13
β-strand	104	1	11
β-strand	109	1	11
β-strand	112-114	3	13
α-helix	119-121	3
β-strand	123-130	8	12
β-strand	138	1	12
β-strand	142-146	5	12

Chain D: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	29-31	3	1
β-strand	36-40	5	2
β-strand	50-60	11	3
β-strand	68-73	6	3
β-strand	78-80	3	3
β-strand	90-92	3	2
β-strand	104-108	5	2
β-strand	117-128	12	3
β-strand	134-144	11	3
β-strand	145-147	3	1
α-helix	154-189	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium channel subunit beta-1	D	protein	218	Homo sapiens	Q07699 (AlphaFold model)
Sodium channel protein type 8 subunit alpha	B	protein	1980	Homo sapiens	Q9UQD0 (AlphaFold model)
Sodium channel subunit beta-2	C	protein	215	Homo sapiens	O60939 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>8GZ2_1 Sodium channel subunit beta-1 (chains D)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE

Sequence of entity 2 (B), FASTA

>8GZ2_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

>8GZ2_3 Sodium channel subunit beta-2 (chains C)
MHRDAWLPRPAFSLTGLSLFFSLVPPGRSMEVTVPATLNVLNGSDARLPCTFNSCYTVNH
KQFSLNWTYQECNNCSEEMFLQFRMKIINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPE
DEGIYNCYIMNPPDRHRGHGKIHLQVLMEEPPERDSTVAVIVGASVGGFLAVVILVLMVV
KCVRRKKEQKLSTDDLKTEEEGKTDGEGNPDDGAK

Ligands and cofactors

ID	Name	Formula	Copies
WMK	(1R,2S,3S,4R,5R,9S,11S,12S,14R)-7-amino-2,4,12-trihydroxy-2-(hydroxymethyl)-10,…	C11 H15 N3 O7	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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:

7W9K 2.2 Å, Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution
25II 2.5 Å, Cryo-EM structure of human Nav1.6 in complex with Iota-Conotoxin RXIA
8I5Y 2.6 Å, Structure of human Nav1.7 in complex with vixotrigine
21TQ 2.7 Å, The structure of Nav1.7 with veratridine standing near the IFM motif (site I)
7XVE 2.7 Å, Human Nav1.7 mutant class-I
8I5B 2.7 Å, Structure of human Nav1.7 in complex with bupivacaine
8I5G 2.7 Å, Structure of human Nav1.7 in complex with PF-05089771
8THH 2.7 Å, Cryo-EM structure of Nav1.7 with LTG
25IH 2.8 Å, Cryo-EM structure of human Nav1.6 in complex with Cn2
7XVF 2.8 Å, Nav1.7 mutant class2
8G1A 2.8 Å, Cryo-EM structure of Nav1.7 with CBD
8XMM 2.89 Å, Voltage-gated sodium channel Nav1.7 variant M9

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