21TP: Sodium channel protein type 9 subunit alpha

Open-state structure of veratridine-activated human Nav1.7. Determined by electron microscopy at 3.0 Å resolution. Released 25 Mar 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 12,524
Mol. weight: 271.25 kDa
Ligands: NAG, LPE, PCW, A1E26
Released: 25 Mar 2026

Explore 21TP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

21TP contains 71 α-helices and 41 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: 64 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	1
α-helix	19-33	15
α-helix	51-53	3
α-helix	57-59	3
α-helix	68-70	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	114-123	10
α-helix	126-142	17
α-helix	152-172	21
α-helix	188-204	17
α-helix	210-214	5
α-helix	215-222	8
α-helix	223-227	5
α-helix	231-266	36
α-helix	270-272	3
β-strand	273-277	5	2
α-helix	286-290	5
α-helix	296-302	7
β-strand	303	1	2
α-helix	312-314	3
β-strand	328-332	5	2
α-helix	347-359	13
α-helix	363-374	12
α-helix	376-378	3
α-helix	379-413	35
α-helix	735-741	7
α-helix	744-761	18
α-helix	770-796	27
α-helix	800-803	4
α-helix	807-823	17
α-helix	832-836	5
α-helix	837-847	11
α-helix	850-863	14
α-helix	867-894	28
α-helix	896-899	4
α-helix	913-925	13
α-helix	929-939	11
α-helix	941-972	32
α-helix	1176-1189	14
α-helix	1192-1207	16
α-helix	1208-1211	4
α-helix	1214-1218	5
α-helix	1220-1247	28
α-helix	1249-1254	6
α-helix	1257-1278	22
α-helix	1286-1290	5
α-helix	1291-1300	10
α-helix	1305-1342	38
β-strand	1351-1352	2	3
β-strand	1357-1358	2	3
α-helix	1359-1360	2
β-strand	1366	1	4
α-helix	1367-1376	10
β-strand	1380-1381	2	3
α-helix	1392-1404	13
α-helix	1408-1416	9
β-strand	1423	1	4
α-helix	1431-1433	3
α-helix	1434-1440	7
α-helix	1441-1447	7
α-helix	1448-1460	13
α-helix	1503-1512	10
α-helix	1515-1534	20
α-helix	1541-1569	29
α-helix	1570-1575	6
α-helix	1577-1601	25
α-helix	1608-1613	6
α-helix	1614-1624	11
α-helix	1628-1639	12
α-helix	1641-1665	25
α-helix	1684-1695	12
α-helix	1700-1707	8
β-strand	1720	1	5
β-strand	1727	1	5
α-helix	1733-1759	27

Chain B: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	6
β-strand	29-31	3	7
β-strand	36-38	3	8
β-strand	40	1	6
β-strand	41	1	9
β-strand	50-60	11	10
β-strand	68-74	7	10
β-strand	77-80	4	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	118-129	12	10
β-strand	132-143	12	10
β-strand	145-147	3	7
α-helix	154-191	38

Chain C: 4 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
α-helix	57-58	2
β-strand	64-70	7	12
α-helix	76-77	2
β-strand	78-83	6	12
β-strand	88	1	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	1988	Homo sapiens	Q15858 (AlphaFold model)
Sodium channel regulatory subunit beta-1	B	protein	173	Homo sapiens	Q07699 (AlphaFold model)
Sodium channel regulatory subunit beta-2	C	protein	119	Homo sapiens	O60939 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>21TP_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

>21TP_2 Sodium channel regulatory subunit beta-1 (chains B)
GCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFRQKGTEEFVKILRYENEVLQ
LEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYECHVYRLLFFENYEHNTSVV
KKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIYCYKKIAAATETA

Sequence of entity 3 (C), FASTA

>21TP_3 Sodium channel regulatory subunit beta-2 (chains C)
MEVTVPATLNVLNGSDARLPCTFNSCYTVNHKQFSLNWTYQECNNCSEEMFLQFRMKIIN
LKLERFQDRVEFSGNPSKYDVSVMLRNVQPEDEGIYNCYIMNPPDRHRGHGKIHLQVLM

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
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	2
A1E26	Veratridine	C36 H51 N O11	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	4

Primary citation

Open-state structure of veratridine-activated human Nav1.7 reveals the molecular choreography of fast inactivation. Fan, X., Chen, J., Xue, L. et al. To be published.

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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