7W9T: Human Nav1.7(E406K)

Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin (S6IV alpha helix conformer). Determined by electron microscopy at 3.0 Å resolution. Released 25 May 2022.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 14,841
Mol. weight: 298.63 kDa
Ligands: 9Z9, Y01, P5S, NAG
Released: 25 May 2022

Explore 7W9T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7W9T contains 96 α-helices and 47 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: 87 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	1
α-helix	17-31	15
β-strand	58	1	2
α-helix	61-63	3
α-helix	66-67	2
β-strand	75-76	2	1
α-helix	80-83	4
β-strand	87-91	5	1
β-strand	96	1	2
β-strand	97-101	5	1
α-helix	104	1
β-strand	105	1	3
β-strand	109	1	3
α-helix	114-123	10
α-helix	127-143	17
α-helix	151-171	21
α-helix	183-185	3
α-helix	187-205	19
α-helix	210-215	6
α-helix	216-218	3
α-helix	219-222	4
α-helix	223-226	4
α-helix	231-243	13
α-helix	246-267	22
α-helix	270-272	3
β-strand	273-277	5	4
α-helix	286-292	7
α-helix	297-302	6
β-strand	303	1	4
β-strand	314	1	4
β-strand	328-332	5	4
α-helix	338-340	3
α-helix	347-358	12
α-helix	363-373	11
α-helix	376-378	3
α-helix	379-385	7
α-helix	386-393	8
α-helix	394-431	38
α-helix	729-740	12
α-helix	743-761	19
α-helix	770-797	28
α-helix	800-805	6
α-helix	807-824	18
α-helix	828-830	3
α-helix	831-839	9
α-helix	840-847	8
α-helix	850-864	15
α-helix	867-894	28
α-helix	896-898	3
α-helix	913-925	13
α-helix	929-939	11
α-helix	941-950	10
α-helix	951-955	5
α-helix	956-970	15
α-helix	973-976	4
α-helix	987-1013	27
α-helix	1176-1189	14
α-helix	1192-1207	16
α-helix	1208-1211	4
α-helix	1220-1248	29
α-helix	1250-1254	5
α-helix	1258-1278	21
α-helix	1285-1289	5
α-helix	1290-1300	11
α-helix	1305-1343	39
β-strand	1349-1352	4	5
β-strand	1357	1	5
β-strand	1366	1	6
α-helix	1367-1376	10
β-strand	1380-1383	4	5
α-helix	1384-1385	2
α-helix	1392-1403	12
α-helix	1408-1416	9
β-strand	1423	1	6
α-helix	1424-1425	2
α-helix	1431-1433	3
α-helix	1434-1441	8
α-helix	1442-1448	7
α-helix	1449-1466	18
α-helix	1476-1487	12
α-helix	1495-1500	6
α-helix	1503-1512	10
α-helix	1515-1533	19
α-helix	1541-1569	29
α-helix	1570-1575	6
α-helix	1577-1601	25
α-helix	1606-1613	8
α-helix	1614-1616	3
α-helix	1617-1620	4
α-helix	1621-1625	5
α-helix	1628-1639	12
α-helix	1641-1666	26
α-helix	1684-1695	12
α-helix	1700-1707	8
α-helix	1719-1721	3
α-helix	1733-1767	35
α-helix	1776-1789	14
β-strand	1796-1798	3	7
α-helix	1799-1805	7
α-helix	1809-1810	2
α-helix	1820-1825	6
β-strand	1829-1831	3	7
β-strand	1835-1837	3	7
α-helix	1838-1850	13
α-helix	1854-1868	15
α-helix	1874-1876	3
β-strand	1879-1882	4	7
α-helix	1883-1890	8

Chain B: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
β-strand	29-31	3	8
β-strand	36-38	3	9
β-strand	50-51	2	10
β-strand	55-61	7	11
β-strand	68-74	7	11
β-strand	77-80	4	11
α-helix	84-86	3
β-strand	90-92	3	9
β-strand	106-108	3	9
α-helix	113-115	3
β-strand	117-123	7	11
β-strand	126-128	3	10
β-strand	133-135	3	10
β-strand	138-144	7	11
β-strand	145-147	3	8
α-helix	151-153	3
α-helix	154-191	38

Chain C: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	12
β-strand	37-41	5	13
β-strand	46-48	3	14
β-strand	51-53	3	12
β-strand	64-70	7	13
β-strand	78-84	7	13
β-strand	86-89	4	13
α-helix	93-95	3
β-strand	99-101	3	14
β-strand	104	1	12
α-helix	105-107	3
β-strand	109	1	12
β-strand	112-114	3	14
α-helix	119-121	3
β-strand	123-130	8	13
α-helix	137	1
β-strand	138-147	10	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium channel protein type 9 subunit alpha	A	protein	2031	Homo sapiens	Q15858 (AlphaFold model)
Sodium channel subunit beta-1	B	protein	218	Homo sapiens	Q07699 (AlphaFold model)
Sodium channel subunit beta-2	C	protein	215	Homo sapiens	O60939 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7W9T_1 Sodium channel protein type 9 subunit alpha (chains A)
MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMAMLPPPGPQSFVHFTK
QSLALIEQRIAERKSKEPKEEKKDDDEEAPKPSSDLEAGKQLPFIYGDIPPGMVSEPLED
LDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRISIKILVHSLFSMLIMCTIL
TNCIFMTMNNPPDWTKNVEYTFTGIYTFESLVKILARGFCVGEFTFLRDPWNWLDFVVIV
FAYLTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLS
VFALIGLQLFMGNLKHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGF
STDSGQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTLRAAGKT
YMIFFVVVIFLGSFYLINLILAVVAMAYKEQNQANIEEAKQKELEFQQMLDRLKKEQEEA
EAIAAAAAEYTSIRRSRIMGLSESSSETSKLSSKSAKERRNRRKKKNQKKLSSGEEKGDA
EKLSKSESEDSIRRKSFHLGVEGHRRAHEKRLSTPNQSPLSIRGSLFSARRSSRTSLFSF
KGRGRDIGSETEFADDEHSIFGDNESRRGSLFVPHRPQERRSSNISQASRSPPMLPVNGK
MHSAVDCNGVVSLVDGRSALMLPNGQLLPEVIIDKATSDDSGTTNQIHKKRRCSSYLLSE
DMLNDPNLRQRAMSRASILTNTVEELEESRQKCPPWWYRFAHKFLIWNCSPYWIKFKKCI
YFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGNLVFTGIFAAEMVLKLIA
MDPYEYFQVGWNIFDSLIVTLSLVELFLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIK
IIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKINDDCTLPRWHMNDFFHSF
LIVFRVLCGEWIETMWDCMEVAGQAMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLT
AIEEDPDANNLQIAVTRIKKGINYVKQTLREFILKAFSKKPKISREIRQAEDLNTKKENY
ISNHTLAEMSKGHNFLKEKDKISGFGSSVDKHLMEDSDGQSFIHNPSLTVTVPIAPGESD
LENMNAEELSSDSDSEYSKVRLNRSSSSECSTVDNPLPGEGEEAEAEPMNSDEPEACFTD
GCVWRFSCCQVNIESGKGKIWWNIRKTCYKIVEHSWFESFIVLMILLSSGALAFEDIYIE
RKKTIKIILEYADKIFTYIFILEMLLKWIAYGYKTYFTNAWCWLDFLIVDVSLVTLVANT
LGYSDLGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSI
MGVNLFAGKFYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLGYL
SLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVFIIFGSFFTLNLFIGVII
DNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPGNKIQGCIFDLVTNQAF
DISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHYYFTVG
WNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFAL
MMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICLFQITTS
AGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYIIISFLVVVNMYIA
VILENFSVATEESTEPLSEDDFEMFYEVWEKFDPDATQFIEFSKLSDFAAALDPPLLIAK
PNKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGESGEMDSLRSQMEERFMSANPSKVSY
EPITTTLKRKQEDVSATVIQRAYRRYRLRQNVKNISSIYIKDGDRDDDLLNKKDMAFDNV
NENSSPEKTDATSSTTSPPSYDSVTKPDKEKYEQDRTEKEDKGKDSKESKK

Sequence of entity 2 (B), FASTA

>7W9T_2 Sodium channel subunit beta-1 (chains B)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE

Sequence of entity 3 (C), FASTA

>7W9T_3 Sodium channel subunit beta-2 (chains C)
MHRDAWLPRPAFSLTGLSLFFSLVPPGRSMEVTVPATLNVLNGSDARLPCTFNSCYTVNH
KQFSLNWTYQECNNCSEEMFLQFRMKIINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPE
DEGIYNCYIMNPPDRHRGHGKIHLQVLMEEPPERDSTVAVIVGASVGGFLAVVILVLMVV
KCVRRKKEQKLSTDDLKTEEEGKTDGEGNPDDGAK

Ligands and cofactors

ID	Name	Formula	Copies
9Z9	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en	C34 H56 O5	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	5
P5S	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine	C42 H82 N O10 P	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
9SL	[(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1…	C10 H17 N7 O4	1
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	5
LPE	1-O-octadecyl-sn-glycero-3-phosphocholine	C26 H57 N O6 P	14

Primary citation

High-resolution structures of human Na v 1.7 reveal gating modulation through alpha-pi helical transition of S6 IV. Huang, G., Liu, D., Wang, W. et al. Cell Rep (2022) 39:110735-110735. DOI 10.1016/j.celrep.2022.110735 · PubMed

Other PDB entries of the same protein (UniProt Q15858 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8YHZ 1.62 Å, The co-crystal structure of the Fab fragment of Ab-1080 with NaV1.7 VSDII peptide
9Y7F 1.7 Å, Crystal structure of nanobody R3D8 in complex with human voltage-gated sodium channel…
7W9K 2.2 Å, Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution
8F0P 2.2 Å, Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-1305
8F0Q 2.5 Å, Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the acylsulfonamide inhibitor…
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
7XVF 2.8 Å, Nav1.7 mutant class2

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