7W9M: Human Nav1.7(E406K)

Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits, ProTx-II and tetrodotoxin (S6IV pi 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: 14,219
Mol. weight: 286.53 kDa
Ligands: LPE, Y01, P5S, NAG
Released: 25 May 2022

Explore 7W9M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7W9M contains 92 α-helices and 43 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: 84 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	1
α-helix	17-33	17
α-helix	51-53	3
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	88-91	4	1
β-strand	96	1	2
β-strand	97-99	3	1
α-helix	104	1
β-strand	105	1	3
β-strand	109	1	3
α-helix	114-123	10
α-helix	126-143	18
α-helix	152-174	23
α-helix	183-185	3
α-helix	187-204	18
α-helix	214-218	5
α-helix	219-222	4
α-helix	223-226	4
α-helix	231-243	13
α-helix	246-267	22
β-strand	273-277	5	4
α-helix	286-290	5
α-helix	296-299	4
β-strand	303	1	4
α-helix	322-325	4
β-strand	328-332	5	4
α-helix	335-336	2
α-helix	338-340	3
α-helix	347-358	12
α-helix	363-374	12
α-helix	376-378	3
α-helix	379-384	6
α-helix	385-391	7
α-helix	392-434	43
α-helix	729-737	9
α-helix	738-740	3
α-helix	743-747	5
α-helix	748-762	15
α-helix	770-803	34
α-helix	807-824	18
α-helix	832-837	6
α-helix	838-844	7
α-helix	850-863	14
α-helix	867-894	28
α-helix	913-924	12
α-helix	929-938	10
α-helix	941-976	36
α-helix	985-986	2
α-helix	987-1013	27
α-helix	1176-1188	13
α-helix	1192-1207	16
α-helix	1208-1211	4
α-helix	1220-1253	34
α-helix	1257-1278	22
α-helix	1285-1290	6
α-helix	1291-1300	10
α-helix	1305-1343	39
β-strand	1349-1352	4	5
β-strand	1357-1358	2	5
α-helix	1359	1
β-strand	1366	1	6
α-helix	1367-1376	10
β-strand	1380-1383	4	5
α-helix	1392-1403	12
α-helix	1408-1416	9
β-strand	1423	1	6
α-helix	1424-1425	2
α-helix	1434-1440	7
α-helix	1441-1447	7
α-helix	1448-1466	19
α-helix	1476-1486	11
α-helix	1493-1500	8
α-helix	1503-1512	10
α-helix	1515-1533	19
α-helix	1542-1568	27
α-helix	1577-1602	26
α-helix	1606-1613	8
α-helix	1614-1619	6
α-helix	1621-1625	5
α-helix	1630-1665	36
α-helix	1666-1668	3
α-helix	1684-1695	12
α-helix	1700-1708	9
α-helix	1733-1747	15
α-helix	1748-1752	5
α-helix	1753-1766	14
α-helix	1779-1789	11
β-strand	1796-1798	3	7
α-helix	1799-1805	7
α-helix	1810	1
α-helix	1816	1
α-helix	1818	1
α-helix	1820-1824	5
β-strand	1829-1831	3	7
β-strand	1835-1837	3	7
α-helix	1838-1850	13
α-helix	1854-1868	15
α-helix	1874-1877	4
β-strand	1879-1882	4	7
α-helix	1883-1890	8

Chain B: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	29-31	3	8
β-strand	36-38	3	9
β-strand	50-61	12	10
β-strand	68-74	7	10
β-strand	77-80	4	10
α-helix	84-86	3
β-strand	90-92	3	9
β-strand	106-108	3	9
α-helix	113-115	3
β-strand	117-128	12	10
β-strand	133-144	12	10
β-strand	145-147	3	8
α-helix	150-153	4
α-helix	154-191	38

Chain C: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	11
β-strand	37-41	5	12
β-strand	46-48	3	13
β-strand	51-52	2	11
β-strand	64-70	7	12
β-strand	78-84	7	12
β-strand	86-89	4	12
α-helix	93-95	3
β-strand	99-101	3	13
β-strand	104	1	11
α-helix	105-107	3
β-strand	109	1	11
β-strand	112-114	3	13
α-helix	119-121	3
β-strand	123-130	8	12
α-helix	137	1
β-strand	138-147	10	12

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

>7W9M_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

>7W9M_2 Sodium channel subunit beta-1 (chains B)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE

Sequence of entity 3 (C), FASTA

>7W9M_3 Sodium channel subunit beta-2 (chains C)
MHRDAWLPRPAFSLTGLSLFFSLVPPGRSMEVTVPATLNVLNGSDARLPCTFNSCYTVNH
KQFSLNWTYQECNNCSEEMFLQFRMKIINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPE
DEGIYNCYIMNPPDRHRGHGKIHLQVLMEEPPERDSTVAVIVGASVGGFLAVVILVLMVV
KCVRRKKEQKLSTDDLKTEEEGKTDGEGNPDDGAK

Ligands and cofactors

ID	Name	Formula	Copies
LPE	1-O-octadecyl-sn-glycero-3-phosphocholine	C26 H57 N O6 P	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	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
9SR	(1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diaz…	C11 H17 N3 O8	1

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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