8I5X: Human Nav1.7

Structure of human Nav1.7 in complex with Vinpocetine. Determined by electron microscopy at 2.9 Å resolution. Released 14 Jun 2023.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 13,590
Mol. weight: 296.06 kDa
Ligands: NAG, P5S, Y01, 9Z9
Released: 14 Jun 2023

Explore 8I5X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I5X contains 84 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: 76 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	1
α-helix	17-33	17
β-strand	57-58	2	1
α-helix	59-60	2
α-helix	61-63	3
α-helix	66-67	2
β-strand	75	1	1
α-helix	80-83	4
β-strand	87-91	5	1
β-strand	96-101	6	1
β-strand	105	1	2
β-strand	109	1	2
α-helix	114-123	10
α-helix	126-143	18
α-helix	152-174	23
α-helix	189-205	17
α-helix	210-217	8
α-helix	218-223	6
α-helix	224-227	4
α-helix	231-243	13
α-helix	246-267	22
α-helix	270-272	3
β-strand	273-277	5	3
α-helix	286-291	6
α-helix	296-299	4
β-strand	303	1	3
α-helix	312-314	3
α-helix	324-325	2
β-strand	328-332	5	3
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	394-417	24
α-helix	729-740	12
α-helix	743-747	5
α-helix	748-761	14
α-helix	770-797	28
α-helix	800-803	4
α-helix	807-824	18
α-helix	834-847	14
α-helix	850-862	13
α-helix	867-894	28
α-helix	896-898	3
α-helix	913-925	13
α-helix	929-939	11
α-helix	941-968	28
α-helix	969-973	5
α-helix	985-986	2
α-helix	987-1013	27
α-helix	1176-1189	14
α-helix	1192-1208	17
α-helix	1209-1211	3
α-helix	1216-1218	3
α-helix	1220-1248	29
α-helix	1250-1255	6
α-helix	1257-1277	21
α-helix	1284-1289	6
α-helix	1290-1300	11
α-helix	1305-1343	39
β-strand	1351-1352	2	4
β-strand	1357-1358	2	4
α-helix	1359-1360	2
β-strand	1366	1	5
α-helix	1367-1376	10
β-strand	1380-1381	2	4
α-helix	1392-1404	13
α-helix	1408-1417	10
β-strand	1423	1	5
α-helix	1431-1433	3
α-helix	1434-1441	8
α-helix	1442-1447	6
α-helix	1448-1466	19
α-helix	1476-1486	11
α-helix	1488-1490	3
α-helix	1491-1500	10
α-helix	1503-1512	10
α-helix	1515-1534	20
α-helix	1541-1569	29
α-helix	1570-1573	4
α-helix	1577-1602	26
α-helix	1606-1613	8
α-helix	1614-1616	3
α-helix	1617-1620	4
α-helix	1621-1625	5
α-helix	1628-1665	38
α-helix	1684-1695	12
α-helix	1700-1707	8
β-strand	1720	1	6
β-strand	1727	1	6
α-helix	1733-1766	34

Chain B: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	29-31	3	7
β-strand	36-38	3	8
β-strand	41	1	9
β-strand	50-61	12	10
β-strand	68-73	6	10
β-strand	78-80	3	10
α-helix	84-86	3
β-strand	90-92	3	8
β-strand	103	1	9
β-strand	106-108	3	8
α-helix	113-115	3
β-strand	117-129	13	10
β-strand	132-135	4	10
β-strand	138-144	7	10
β-strand	145-147	3	7
α-helix	151-153	3
α-helix	154-191	38

Chain C: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	11
β-strand	37-41	5	12
β-strand	46-48	3	13
β-strand	51-53	3	11
β-strand	64-70	7	12
α-helix	76	1
β-strand	77-83	7	12
β-strand	87-89	3	12
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
β-strand	138-147	10	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium channel protein type 9 subunit alpha	A	protein	2028	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

>8I5X_1 Sodium channel protein type 9 subunit alpha (chains A)
WSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMAMLPPPGPQSFVHFTKQSL
ALIEQRIAERKSKEPKEEKKDDDEEAPKPSSDLEAGKQLPFIYGDIPPGMVSEPLEDLDP
YYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRISIKILVHSLFSMLIMCTILTNC
IFMTMNNPPDWTKNVEYTFTGIYTFESLVKILARGFCVGEFTFLRDPWNWLDFVVIVFAY
LTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFA
LIGLQLFMGNLKHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGFSTD
SGQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTLRAAGKTYMI
FFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQKELEFQQMLDRLKKEQEEAEAI
AAAAAEYTSIRRSRIMGLSESSSETSKLSSKSAKERRNRRKKKNQKKLSSGEEKGDAEKL
SKSESEDSIRRKSFHLGVEGHRRAHEKRLSTPNQSPLSIRGSLFSARRSSRTSLFSFKGR
GRDIGSETEFADDEHSIFGDNESRRGSLFVPHRPQERRSSNISQASRSPPMLPVNGKMHS
AVDCNGVVSLVDGRSALMLPNGQLLPEVIIDKATSDDSGTTNQIHKKRRCSSYLLSEDML
NDPNLRQRAMSRASILTNTVEELEESRQKCPPWWYRFAHKFLIWNCSPYWIKFKKCIYFI
VMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGNLVFTGIFAAEMVLKLIAMDP
YEYFQVGWNIFDSLIVTLSLVELFLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIG
NSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIV
FRVLCGEWIETMWDCMEVAGQAMCLIVYMMVMVIGNLVVLNLFLALLLSSFSSDNLTAIE
EDPDANNLQIAVTRIKKGINYVKQTLREFILKAFSKKPKISREIRQAEDLNTKKENYISN
HTLAEMSKGHNFLKEKDKISGFGSSVDKHLMEDSDGQSFIHNPSLTVTVPIAPGESDLEN
MNAEELSSDSDSEYSKVRLNRSSSSECSTVDNPLPGEGEEAEAEPMNSDEPEACFTDGCV
WRFSCCQVNIESGKGKIWWNIRKTCYKIVEHSWFESFIVLMILLSSGALAFEDIYIERKK
TIKIILEYADKIFTYIFILEMLLKWIAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGY
SDLGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGV
NLFAGKFYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLGYLSLL
QVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVFIIFGSFFTLNLFIGVIIDNF
NQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPGNKIQGCIFDLVTNQAFDIS
IMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHYYFTVGWNI
FDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFALMMS
LPALFNIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICLFQITTSAGW
DGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYIIISFLVVVNMYIAVIL
ENFSVATEESTEPLSEDDFEMFYEVWEKFDPDATQFIEFSKLSDFAAALDPPLLIAKPNK
VQLIAMDLPMVSGDRIHCLDILFAFTKRVLGESGEMDSLRSQMEERFMSANPSKVSYEPI
TTTLKRKQEDVSATVIQRAYRRYRLRQNVKNISSIYIKDGDRDDDLLNKKDMAFDNVNEN
SSPEKTDATSSTTSPPSYDSVTKPDKEKYEQDRTEKEDKGKDSKESKK

Sequence of entity 2 (B), FASTA

>8I5X_2 Sodium channel subunit beta-1 (chains B)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE

Sequence of entity 3 (C), FASTA

>8I5X_3 Sodium channel subunit beta-2 (chains C)
MHRDAWLPRPAFSLTGLSLFFSLVPPGRSMEVTVPATLNVLNGSDARLPCTFNSCYTVNH
KQFSLNWTYQECNNCSEEMFLQFRMKIINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPE
DEGIYNCYIMNPPDRHRGHGKIHLQVLMEEPPERDSTVAVIVGASVGGFLAVVILVLMVV
KCVRRKKEQKLSTDDLKTEEEGKTDGEGNPDDGAK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5
P5S	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine	C42 H82 N O10 P	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	5
9Z9	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en	C34 H56 O5	1
T7F	Vinpocetine	C22 H26 N2 O2	1
LPE	1-O-octadecyl-sn-glycero-3-phosphocholine	C26 H57 N O6 P	11
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	5

Primary citation

Structural mapping of Na v 1.7 antagonists. Wu, Q., Huang, J., Fan, X. et al. Nat Commun (2023) 14:3224-3224. DOI 10.1038/s41467-023-38942-3 · 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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