8THG: Nav1.7 with RLZ

Cryo-EM structure of Nav1.7 with RLZ. Determined by electron microscopy at 2.9 Å resolution. Released 22 Nov 2023.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 3
Atoms: 13,168
Mol. weight: 284.43 kDa
Ligands: PCW, LPE, Y01, 657
Released: 22 Nov 2023

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

Secondary structure: helices and β-sheets

8THG contains 86 α-helices and 40 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: 78 helices, 15 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	1
α-helix	59-60	2
α-helix	61-63	3
α-helix	66-67	2
α-helix	68-70	3
β-strand	74-76	3	1
α-helix	80-83	4
β-strand	88-92	5	1
β-strand	96-99	4	1
α-helix	104	1
α-helix	105-107	3
α-helix	114-124	11
α-helix	126-142	17
α-helix	154-174	21
α-helix	187-205	19
α-helix	210-215	6
α-helix	216-218	3
α-helix	219-227	9
α-helix	231-242	12
α-helix	247-266	20
α-helix	270-272	3
β-strand	273-277	5	2
α-helix	286-290	5
α-helix	296-299	4
β-strand	303	1	2
α-helix	312-314	3
α-helix	324-325	2
β-strand	328-332	5	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	386-390	5
α-helix	393-417	25
α-helix	730-741	12
α-helix	744-761	18
α-helix	770-803	34
α-helix	807-824	18
α-helix	834-846	13
α-helix	850-862	13
α-helix	867-894	28
α-helix	896-898	3
α-helix	913-925	13
α-helix	930-939	10
α-helix	941-973	33
α-helix	974-976	3
α-helix	987-1013	27
α-helix	1176-1189	14
α-helix	1192-1207	16
α-helix	1208-1211	4
α-helix	1214-1218	5
α-helix	1220-1248	29
α-helix	1250-1254	5
α-helix	1257-1278	22
α-helix	1285-1289	5
α-helix	1290-1300	11
α-helix	1305-1343	39
β-strand	1349-1352	4	3
β-strand	1357-1358	2	3
α-helix	1359-1360	2
β-strand	1366	1	4
α-helix	1367-1376	10
β-strand	1380-1383	4	3
α-helix	1392-1403	12
α-helix	1408-1417	10
β-strand	1423	1	4
α-helix	1431-1433	3
α-helix	1434-1442	9
α-helix	1443-1447	5
α-helix	1448-1467	20
α-helix	1476-1486	11
α-helix	1487-1489	3
α-helix	1491-1500	10
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	1606-1612	7
α-helix	1613-1616	4
α-helix	1617-1620	4
α-helix	1621-1626	6
α-helix	1628-1665	38
α-helix	1684-1695	12
α-helix	1700-1704	5
α-helix	1705-1708	4
β-strand	1720	1	5
β-strand	1727	1	5
α-helix	1733-1767	35

Chain B: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	29-31	3	6
β-strand	36-38	3	7
β-strand	41	1	8
β-strand	54-61	8	9
β-strand	68-74	7	9
β-strand	77-80	4	9
β-strand	90-92	3	7
β-strand	103	1	8
β-strand	106-108	3	7
α-helix	113-115	3
β-strand	117-129	13	9
β-strand	132-144	13	9
β-strand	145-147	3	6
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	10
β-strand	37-41	5	11
β-strand	47-48	2	12
β-strand	51-53	3	10
α-helix	57-58	2
β-strand	64-70	7	11
α-helix	76	1
β-strand	77-83	7	11
β-strand	87-89	3	11
β-strand	99-101	3	12
β-strand	104	1	10
α-helix	105-107	3
β-strand	109	1	10
β-strand	112-114	3	12
α-helix	119-121	3
β-strand	123-130	8	11
β-strand	138-147	10	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium channel protein type 9 subunit alpha	A	protein	1988	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

>8THG_1 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

Sequence of entity 2 (B), FASTA

>8THG_2 Sodium channel subunit beta-1 (chains B)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE

Sequence of entity 3 (C), FASTA

>8THG_3 Sodium channel subunit beta-2 (chains C)
MHRDAWLPRPAFSLTGLSLFFSLVPPGRSMEVTVPATLNVLNGSDARLPCTFNSCYTVNH
KQFSLNWTYQECNNCSEEMFLQFRMKIINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPE
DEGIYNCYIMNPPDRHRGHGKIHLQVLMEEPPERDSTVAVIVGASVGGFLAVVILVLMVV
KCVRRKKEQKLSTDDLKTEEEGKTDGEGNPDDGAK

Ligands and cofactors

ID	Name	Formula	Copies
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	1
LPE	1-O-octadecyl-sn-glycero-3-phosphocholine	C26 H57 N O6 P	6
Y01	Cholesterol hemisuccinate	C31 H50 O4	3
657	6-(trifluoromethoxy)-1,3-benzothiazol-2-amine	C8 H5 F3 N2 O S	1
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

Primary citation

Dual-pocket inhibition of Na v channels by the antiepileptic drug lamotrigine. Huang, J., Fan, X., Jin, X. et al. Proc Natl Acad Sci U S A (2023) 120:e2309773120-e2309773120. DOI 10.1073/pnas.2309773120 · 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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