7W9K: Human Nav1.7-beta1-beta2 complex

Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution. Determined by electron microscopy at 2.2 Å resolution. Released 1 Jun 2022.

Method: Electron microscopy
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 3
Atoms: 14,933
Mol. weight: 300.56 kDa
Ligands: P5S, Y01, 9Z9, LPE
Released: 1 Jun 2022

Explore 7W9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7W9K contains 90 α-helices and 48 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: 81 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	1
α-helix	17-33	17
β-strand	58	1	2
α-helix	61-63	3
α-helix	66-67	2
β-strand	75	1	1
α-helix	80-84	5
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	126-143	18
α-helix	150-152	3
α-helix	153-174	22
α-helix	183-185	3
α-helix	189-205	17
α-helix	210-221	12
α-helix	223-227	5
α-helix	231-244	14
α-helix	246-267	22
α-helix	270-272	3
β-strand	273-277	5	4
α-helix	286-291	6
α-helix	296-299	4
β-strand	303	1	4
α-helix	312-314	3
α-helix	324-325	2
β-strand	328-332	5	4
α-helix	335-336	2
α-helix	347-359	13
α-helix	363-374	12
α-helix	376-378	3
α-helix	379-385	7
α-helix	386-393	8
α-helix	394-434	41
α-helix	729-740	12
α-helix	746-761	16
α-helix	770-797	28
α-helix	800-803	4
α-helix	807-824	18
α-helix	834-846	13
α-helix	852-862	11
α-helix	867-894	28
α-helix	896-899	4
α-helix	913-925	13
α-helix	929-939	11
α-helix	941-968	28
α-helix	969-973	5
α-helix	987-1013	27
α-helix	1176-1189	14
α-helix	1192-1209	18
α-helix	1216-1218	3
α-helix	1220-1254	35
α-helix	1257-1277	21
α-helix	1284-1290	7
α-helix	1291-1299	9
α-helix	1300-1303	4
α-helix	1305-1343	39
β-strand	1348-1352	5	5
β-strand	1357-1358	2	5
β-strand	1366	1	6
α-helix	1367-1376	10
β-strand	1380-1384	5	5
α-helix	1392-1403	12
α-helix	1408-1417	10
β-strand	1423	1	6
α-helix	1431-1433	3
α-helix	1434-1440	7
α-helix	1441-1447	7
α-helix	1448-1466	19
α-helix	1476-1488	13
α-helix	1495-1500	6
α-helix	1503-1512	10
α-helix	1515-1534	20
α-helix	1541-1568	28
α-helix	1570-1575	6
α-helix	1577-1599	23
α-helix	1606-1612	7
α-helix	1613-1616	4
α-helix	1617-1621	5
α-helix	1623-1626	4
α-helix	1631-1639	9
α-helix	1641-1665	25
α-helix	1684-1695	12
α-helix	1700-1707	8
β-strand	1720	1	7
β-strand	1727	1	7
α-helix	1733-1767	35
α-helix	1776-1786	11
β-strand	1796-1798	3	8
α-helix	1799-1805	7
α-helix	1810	1
α-helix	1820-1825	6
β-strand	1829-1830	2	9
β-strand	1831	1	8
β-strand	1835-1837	3	8
α-helix	1838-1850	13
α-helix	1855-1870	16
α-helix	1874-1876	3
β-strand	1881-1882	2	9
α-helix	1883-1890	8

Chain B: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	29-31	3	10
β-strand	36-38	3	11
β-strand	41	1	12
β-strand	51-61	11	13
β-strand	68-74	7	13
β-strand	77-80	4	13
α-helix	84-86	3
β-strand	90-92	3	11
β-strand	103	1	12
β-strand	106-108	3	11
α-helix	113-115	3
β-strand	117-128	12	13
β-strand	133-144	12	13
β-strand	145-147	3	10
α-helix	151-153	3
α-helix	154-191	38

Chain C: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	14
β-strand	37-41	5	15
β-strand	46-48	3	16
β-strand	51-52	2	14
β-strand	64-70	7	15
β-strand	77-83	7	15
β-strand	87-89	3	15
α-helix	93-95	3
β-strand	99-101	3	16
β-strand	104	1	14
α-helix	105-107	3
β-strand	109	1	14
β-strand	112-114	3	16
α-helix	119-121	3
β-strand	123-130	8	15
α-helix	137	1
β-strand	138-147	10	15

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

>7W9K_1 Sodium channel protein type 9 subunit alpha (chains A)
MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMAMLPPPGPQSFVHFTK
QSLALIEQRIAERKSKEPKEEKKDDDEEAPKPSSDLEAGKQLPFIYGDIPPGMVSEPLED
LDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRISIKILVHSLFSMLIMCTIL
TNCIFMTMNNPPDWTKNVEYTFTGIYTFESLVKILARGFCVGEFTFLRDPWNWLDFVVIV
FAYLTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLS
VFALIGLQLFMGNLKHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGF
STDSGQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTLRAAGKT
YMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQKELEFQQMLDRLKKEQEEA
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

>7W9K_2 Sodium channel subunit beta-1 (chains B)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE

Sequence of entity 3 (C), FASTA

>7W9K_3 Sodium channel subunit beta-2 (chains C)
MHRDAWLPRPAFSLTGLSLFFSLVPPGRSMEVTVPATLNVLNGSDARLPCTFNSCYTVNH
KQFSLNWTYQECNNCSEEMFLQFRMKIINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPE
DEGIYNCYIMNPPDRHRGHGKIHLQVLMEEPPERDSTVAVIVGASVGGFLAVVILVLMVV
KCVRRKKEQKLSTDDLKTEEEGKTDGEGNPDDGAK

Ligands and cofactors

ID	Name	Formula	Copies
P5S	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine	C42 H82 N O10 P	3
Y01	Cholesterol hemisuccinate	C31 H50 O4	6
9Z9	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en	C34 H56 O5	1
LPE	1-O-octadecyl-sn-glycero-3-phosphocholine	C26 H57 N O6 P	15
1PW	(2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate	C20 H40 N O6 P	1
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

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

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…
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
8G1A 2.8 Å, Cryo-EM structure of Nav1.7 with CBD

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