8G1A: Nav1.7 with CBD

Cryo-EM structure of Nav1.7 with CBD. Determined by electron microscopy at 2.8 Å resolution. Released 5 Jul 2023.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 13,725
Mol. weight: 292.86 kDa
Ligands: NAG, P0T, P5S, Y01
Released: 5 Jul 2023

Explore 8G1A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G1A contains 77 α-helices and 34 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: 72 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	17-33	17
α-helix	51-53	3
β-strand	75	1	1
α-helix	80-83	4
β-strand	87-91	5	1
β-strand	97-101	5	1
α-helix	105-107	3
α-helix	114-124	11
α-helix	126-143	18
α-helix	152-163	12
α-helix	167-173	7
α-helix	187-189	3
α-helix	190-202	13
α-helix	210-215	6
α-helix	216-221	6
α-helix	222-227	6
α-helix	231-244	14
α-helix	247-266	20
α-helix	270-272	3
β-strand	274-277	4	2
α-helix	286-289	4
α-helix	296-302	7
β-strand	303	1	2
α-helix	312-314	3
β-strand	328-331	4	2
α-helix	335-336	2
α-helix	347-359	13
α-helix	363-373	11
α-helix	376-378	3
α-helix	379-388	10
α-helix	389-393	5
α-helix	394-434	41
α-helix	731-740	10
α-helix	744-761	18
α-helix	770-795	26
α-helix	807-823	17
α-helix	834-847	14
α-helix	852-863	12
α-helix	867-887	21
α-helix	890-894	5
α-helix	895-898	4
α-helix	913-925	13
α-helix	929-938	10
α-helix	941-968	28
α-helix	969-974	6
α-helix	987-1013	27
α-helix	1177-1188	12
α-helix	1192-1207	16
α-helix	1208-1211	4
α-helix	1216-1218	3
α-helix	1220-1247	28
α-helix	1250-1253	4
α-helix	1257-1278	22
α-helix	1284-1291	8
α-helix	1292-1300	9
α-helix	1305-1315	11
α-helix	1318-1342	25
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	1381-1383	3	3
α-helix	1392-1404	13
α-helix	1408-1416	9
β-strand	1423	1	4
α-helix	1431-1433	3
α-helix	1434-1442	9
α-helix	1443-1447	5
α-helix	1448-1462	15
α-helix	1476-1489	14
α-helix	1491-1498	8
α-helix	1503-1511	9
α-helix	1517-1533	17
α-helix	1541-1568	28
α-helix	1577-1601	25
α-helix	1606-1612	7
α-helix	1617-1621	5
α-helix	1622-1624	3
α-helix	1631-1665	35
α-helix	1684-1695	12
α-helix	1700-1707	8
α-helix	1733-1765	33

Chain B: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	31	1	5
β-strand	36-38	3	6
β-strand	50-61	12	7
β-strand	68-74	7	7
β-strand	77-80	4	7
β-strand	90-92	3	6
β-strand	106-108	3	6
β-strand	117-129	13	7
β-strand	132-144	13	7
β-strand	147	1	5
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	8
β-strand	37-41	5	9
β-strand	46-48	3	10
β-strand	51-53	3	8
α-helix	57-58	2
β-strand	64-70	7	9
α-helix	76	1
β-strand	77-83	7	9
β-strand	87-89	3	9
β-strand	99-101	3	10
β-strand	104	1	8
β-strand	109	1	8
β-strand	112-114	3	10
α-helix	119-121	3
β-strand	123-130	8	9
β-strand	138-147	10	9

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

>8G1A_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

>8G1A_2 Sodium channel subunit beta-1 (chains B)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE

Sequence of entity 3 (C), FASTA

>8G1A_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	6
P0T	cannabidiol	C21 H30 O2	2
P5S	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine	C42 H82 N O10 P	2
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
LPE	1-O-octadecyl-sn-glycero-3-phosphocholine	C26 H57 N O6 P	13
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	4

Primary citation

Cannabidiol inhibits Na v channels through two distinct binding sites. Huang, J., Fan, X., Jin, X. et al. Nat Commun (2023) 14:3613-3613. DOI 10.1038/s41467-023-39307-6 · 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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