8I5G: Human Nav1.7

Structure of human Nav1.7 in complex with PF-05089771. Determined by electron microscopy at 2.7 Å resolution. Released 14 Jun 2023.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 13,389
Mol. weight: 285.4 kDa
Ligands: Y01, 9Z9, LPE, PCW
Released: 14 Jun 2023

Explore 8I5G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I5G contains 80 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: 74 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	8
α-helix	17-33	17
β-strand	58	1	9
α-helix	59-60	2
α-helix	61-63	3
α-helix	65-67	3
β-strand	75	1	8
β-strand	87-91	5	8
β-strand	96	1	9
β-strand	97-101	5	8
β-strand	105	1	10
β-strand	109	1	10
α-helix	114-123	10
α-helix	126-143	18
α-helix	152-174	23
α-helix	187-205	19
α-helix	210-216	7
α-helix	217-224	8
α-helix	231-243	13
α-helix	246-267	22
α-helix	270-272	3
β-strand	273-277	5	11
α-helix	286-290	5
α-helix	296-299	4
β-strand	303	1	11
α-helix	312-314	3
α-helix	324-325	2
β-strand	328-332	5	11
α-helix	335-336	2
α-helix	338-340	3
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	748-760	13
α-helix	761-763	3
α-helix	770-797	28
α-helix	800-803	4
α-helix	807-824	18
α-helix	834-847	14
α-helix	850-863	14
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	987-1013	27
α-helix	1176-1189	14
α-helix	1192-1207	16
α-helix	1208-1211	4
α-helix	1216-1218	3
α-helix	1220-1255	36
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	1349-1352	4	12
β-strand	1357-1358	2	12
α-helix	1359-1360	2
β-strand	1366	1	13
α-helix	1367-1376	10
β-strand	1380-1383	4	12
α-helix	1392-1404	13
α-helix	1408-1416	9
β-strand	1423	1	13
α-helix	1431-1433	3
α-helix	1434-1441	8
α-helix	1442-1447	6
α-helix	1448-1466	19
α-helix	1476-1488	13
α-helix	1491-1500	10
α-helix	1503-1513	11
α-helix	1515-1534	20
α-helix	1541-1569	29
α-helix	1570-1575	6
α-helix	1577-1602	26
α-helix	1606-1612	7
α-helix	1613-1616	4
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	14
β-strand	1727	1	14
α-helix	1733-1766	34

Chain B: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
β-strand	29-31	3	1
β-strand	36-38	3	2
β-strand	41	1	3
β-strand	50-61	12	4
β-strand	68-74	7	4
β-strand	77-80	4	4
β-strand	90-92	3	2
β-strand	103	1	3
β-strand	106-108	3	2
α-helix	113-115	3
β-strand	117-129	13	4
β-strand	132-144	13	4
β-strand	145-147	3	1
α-helix	151-153	3
α-helix	154-191	38

Chain C: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	5
β-strand	37-41	5	6
β-strand	46-48	3	7
β-strand	51-53	3	5
β-strand	64-70	7	6
β-strand	78-83	6	6
β-strand	87-89	3	6
β-strand	99-101	3	7
β-strand	104	1	5
α-helix	105-107	3
β-strand	109	1	5
β-strand	112-114	3	7
α-helix	119-121	3
β-strand	123-130	8	6
β-strand	138-147	10	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium channel subunit beta-1	B	protein	192	Homo sapiens	Q07699 (AlphaFold model)
Sodium channel subunit beta-2	C	protein	215	Homo sapiens	O60939 (AlphaFold model)
Sodium channel protein type 9 subunit alpha	A	protein	1988	Homo sapiens	Q15858 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8I5G_1 Sodium channel subunit beta-1 (chains B)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETA

Sequence of entity 2 (C), FASTA

>8I5G_2 Sodium channel subunit beta-2 (chains C)
MHRDAWLPRPAFSLTGLSLFFSLVPPGRSMEVTVPATLNVLNGSDARLPCTFNSCYTVNH
KQFSLNWTYQECNNCSEEMFLQFRMKIINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPE
DEGIYNCYIMNPPDRHRGHGKIHLQVLMEEPPERDSTVAVIVGASVGGFLAVVILVLMVV
KCVRRKKEQKLSTDDLKTEEEGKTDGEGNPDDGAK

Sequence of entity 3 (A), FASTA

>8I5G_3 Sodium channel protein type 9 subunit alpha (chains A)
MAMLPPPGPQSFVHFTKQSLALIEQRIAERKSKEPKEEKKDDDEEAPKPSSDLEAGKQLP
FIYGDIPPGMVSEPLEDLDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRISI
KILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIYTFESLVKILARGFCVGE
FTFLRDPWNWLDFVVIVFAYLTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQ
SVKKLSDVMILTVFCLSVFALIGLQLFMGNLKHKCFRNSLENNETLESIMNTLESEEDFR
KYFYYLEGSKDALLCGFSTDSGQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQ
DYWENLYQQTLRAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQKE
LEFQQMLDRLKKEQEEAEAIAAAAAEYTSIRRSRIMGLSESSSETSKLSSKSAKERRNRR
KKKNQKKLSSGEEKGDAEKLSKSESEDSIRRKSFHLGVEGHRRAHEKRLSTPNQSPLSIR
GSLFSARRSSRTSLFSFKGRGRDIGSETEFADDEHSIFGDNESRRGSLFVPHRPQERRSS
NISQASRSPPMLPVNGKMHSAVDCNGVVSLVDGRSALMLPNGQLLPEVIIDKATSDDSGT
TNQIHKKRRCSSYLLSEDMLNDPNLRQRAMSRASILTNTVEELEESRQKCPPWWYRFAHK
FLIWNCSPYWIKFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGN
LVFTGIFAAEMVLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLADVEGLSVLRSFRLL
RVFKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKIN
DDCTLPRWHMNDFFHSFLIVFRVLCGEWIETMWDCMEVAGQAMCLIVYMMVMVIGNLVVL
NLFLALLLSSFSSDNLTAIEEDPDANNLQIAVTRIKKGINYVKQTLREFILKAFSKKPKI
SREIRQAEDLNTKKENYISNHTLAEMSKGHNFLKEKDKISGFGSSVDKHLMEDSDGQSFI
HNPSLTVTVPIAPGESDLENMNAEELSSDSDSEYSKVRLNRSSSSECSTVDNPLPGEGEE
AEAEPMNSDEPEACFTDGCVWRFSCCQVNIESGKGKIWWNIRKTCYKIVEHSWFESFIVL
MILLSSGALAFEDIYIERKKTIKIILEYADKIFTYIFILEMLLKWIAYGYKTYFTNAWCW
LDFLIVDVSLVTLVANTLGYSDLGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPS
IMNVLLVCLIFWLIFSIMGVNLFAGKFYECINTTDGSRFPASQVPNRSECFALMNVSQNV
RWKNLKVNFDNVGLGYLSLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVF
IIFGSFFTLNLFIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRP
GNKIQGCIFDLVTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTG
ECVLKLISLRHYYFTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRI
LRLVKGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFN
FETFGNSMICLFQITTSAGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYF
VSYIIISFLVVVNMYIAVILENFSVATEESTEPLSEDDFEMFYEVWEKFDPDATQFIEFS
KLSDFAAALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGESGEMDSLR
SQMEERFMSANPSKVSYEPITTTLKRKQEDVSATVIQRAYRRYRLRQNVKNISSIYIKDG
DRDDDLLNKKDMAFDNVNENSSPEKTDATSSTTSPPSYDSVTKPDKEKYEQDRTEKEDKG
KDSKESKK

Ligands and cofactors

ID	Name	Formula	Copies
Y01	Cholesterol hemisuccinate	C31 H50 O4	2
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	8
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	5
T70	PF-05089771	C18 H12 Cl2 F N5 O3 S2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

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

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 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
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
7W9P 2.9 Å, Cryo-EM structure of human Nav1.7(E406K) in complex with auxiliary beta subunits,…

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