7XVF: Nav1.7 mutant class2

Nav1.7 mutant class2. Determined by electron microscopy at 2.8 Å resolution. Released 10 Aug 2022.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 13,625
Mol. weight: 299.52 kDa
Ligands: 1PW, LPE, CLR, Y01
Released: 10 Aug 2022

Explore 7XVF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7XVF contains 83 α-helices and 37 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, 13 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	1
α-helix	17-33	17
β-strand	58	1	2
α-helix	59-60	2
α-helix	61-63	3
α-helix	66-67	2
β-strand	75	1	1
α-helix	80-84	5
β-strand	87-91	5	1
β-strand	96	1	2
β-strand	97-101	5	1
α-helix	104	1
α-helix	105-107	3
α-helix	114-124	11
α-helix	126-143	18
α-helix	151-174	24
α-helix	183-185	3
α-helix	187-204	18
α-helix	211-218	8
α-helix	220-225	6
α-helix	231-244	14
α-helix	246-267	22
α-helix	270-272	3
β-strand	273-277	5	3
α-helix	286-292	7
α-helix	296-302	7
β-strand	303	1	3
α-helix	312-314	3
β-strand	328-332	5	3
α-helix	338-340	3
α-helix	347-359	13
α-helix	363-374	12
α-helix	376-378	3
α-helix	379-384	6
α-helix	385-391	7
α-helix	392-416	25
α-helix	727-740	14
α-helix	743-761	19
α-helix	770-797	28
α-helix	800-805	6
α-helix	809-823	15
α-helix	832-834	3
α-helix	838-848	11
α-helix	850-894	45
α-helix	896-899	4
α-helix	913-925	13
α-helix	929-939	11
α-helix	941-952	12
α-helix	953-960	8
α-helix	961-971	11
α-helix	987-1013	27
α-helix	1176-1190	15
α-helix	1192-1211	20
α-helix	1220-1247	28
α-helix	1250-1253	4
α-helix	1257-1278	22
α-helix	1284-1291	8
α-helix	1292-1295	4
α-helix	1298-1303	6
α-helix	1305-1315	11
α-helix	1318-1343	26
β-strand	1348-1352	5	4
β-strand	1366	1	5
α-helix	1367-1376	10
β-strand	1380-1384	5	4
α-helix	1392-1404	13
α-helix	1408-1415	8
β-strand	1423	1	5
α-helix	1431-1433	3
α-helix	1434-1442	9
α-helix	1443-1448	6
α-helix	1449-1467	19
α-helix	1476-1489	14
α-helix	1491-1500	10
α-helix	1503-1513	11
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	1617-1621	5
α-helix	1623-1626	4
α-helix	1628-1666	39
α-helix	1684-1695	12
α-helix	1700-1708	9
α-helix	1733-1747	15
α-helix	1748-1752	5
α-helix	1753-1767	15

Chain B: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
β-strand	29-31	3	6
β-strand	36-38	3	7
β-strand	50-61	12	8
α-helix	67	1
β-strand	68-74	7	8
β-strand	77-80	4	8
β-strand	90-92	3	7
β-strand	106-108	3	7
α-helix	113-115	3
β-strand	117-128	12	8
β-strand	133-144	12	8
β-strand	145-147	3	6
α-helix	154-191	38

Chain C: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	9
β-strand	37-40	4	10
β-strand	46-48	3	11
β-strand	51-52	2	9
α-helix	57-59	3
β-strand	64-70	7	10
β-strand	81-83	3	10
β-strand	87-89	3	10
β-strand	99-101	3	11
β-strand	104	1	9
α-helix	105-107	3
β-strand	109	1	9
β-strand	112-114	3	11
α-helix	119-121	3
β-strand	123-131	9	10
β-strand	134-137	4	10
β-strand	140-146	7	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium channel protein type 9 subunit alpha	A	protein	2022	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

>7XVF_1 Sodium channel protein type 9 subunit alpha (chains A)
EKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMAMLPPPGPQSFVHFTKQSLALIEQR
IAERKSKEPKEEKKDDDEEAPKPSSDLEAGKQLPFIYGDIPPGMVSEPLEDLDPYYADKK
TFIVLNKGKTIFRFNATPALYMLSPFSPLRRISIKILVHSLFSMLIMCTILTNCIFMTMN
NPPDWTKNVKYTFTGIYTFESLVKILARGFCVGEFTFLRDPWNWLDFVVIVFAYLTEFVN
LGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLSVFALIGLQL
FMGNLKHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGFSTDSGQCPE
GYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTLRAAGKTYMIFFVVVI
FLGSFYLINLILAVVAMAYEEQNQANIEEAKQKELEFQQMLDRLKKEQEEAEAIAAAAAE
YTSIRRSRIMGLSESSSETSKLSSKSAKERRNRRKKKNQKKLSSGEEKGDAEKLSKSESE
DSIRRKSFHLGVEGHRRAHEKRLSTPNQSPLSIRGSLFSARRSSRTSLFSFKGRGRDIGS
ETEFADDEHSIFGDNESRRGSLFVPHRPQERRSSNISQASRSPPMLPVNGKMHSAVDCNG
VVSLVDGRSALMLPNGQLLPEVIIDKATSDDSGTTNQIHKKRRCSSYLLSEDMLNDPNLR
QRAMSRASILTNTVEELEESRQKCPPWWYRFAHKFLIWNCSPYWIKFKKCIYFIVMDPFV
DLAITICIVLNTLFMAMEHHPMTEEFKNVLAIRNLVFTGIFAAEMVLKLIAMDPYEYFQV
GWNIFDSLIVTLSLVELFLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIKIIGNSVGAF
GNLMLVLFIIVFIFAVVGMQLFGKSYKECVCKINDDCTLPRWHMNDFFHSFLIVFRVLCG
EWIETMWDCMEVAGQAMCLIFYMMVFFIGNLVVLNLFLALLLSSFSSDNLTAIEEDPDAN
NLQIAVTRIKKGINYVKQTLREFILKAFSKKPKISREIRQAEDLNTKKENYISNHTLAEM
SKGHNFLKEKDKISGFGSSVDKHLMEDSDGQSFIHNPSLTVTVPIAPGESDLENMNAEEL
SSDSDSEYSKVRLNRSSSSECSTVDNPLPGEGEEAEAEPMNSDEPEACFTDGCVWRFSCC
QVNIESGKGKIWWNIRKTCYKIVEHSWFESFIVLMILLSSGALAFEDIYIERKKTIKIIL
EYADKIFTYIFILEMLLKWIAYGYKTYFTNAWCWLDFLIVDVSLVTLVANTLGYSDLGPI
KSLRTLRALRPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSIMGVNLFAGK
FYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLGYLSLLQVATFK
GWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFIFFIIFGSFFTLNLFICVIIDNFNQQKKK
LGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPGNKIQGCIFDLVTNQAFDISIMVLIC
LNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHYYFTVGWNIFDFVVV
IISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFALMMSLPALFN
IGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICLFQITTSAGWDGLLAP
ILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYIIISFLVVVNMYIAVILENFSVA
TEESTEPLSEDDFEMFYEVWEKFDPDATQFIEFSKLSDFAAALDPPLLIAKPNKVQLIAM
DLPMVSGDRIHCLDILFAFTKRVLGESGEMDSLRSQMEERFMSANPSKVSYEPITTTLKR
KQEDVSATVIQRAYRRYRLRQNVKNISSIYIKDGDRDDDLLNKKDMAFDNVNENSSPEKT
DATSSTTSPPSYDSVTKPDKEKYEQDRTEKEDKGKDSKESKK

Sequence of entity 2 (B), FASTA

>7XVF_2 Sodium channel subunit beta-1 (chains B)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE

Sequence of entity 3 (C), FASTA

>7XVF_3 Sodium channel subunit beta-2 (chains C)
MHRDAWLPRPAFSLTGLSLFFSLVPPGRSMEVTVPATLNVLNGSDARLPCTFNSCYTVNH
KQFSLNWTYQECNNCSEEMFLQFRMKIINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPE
DEGIYNCYIMNPPDRHRGHGKIHLQVLMEEPPERDSTVAVIVGASVGGFLAVVILVLMVV
KCVRRKKEQKLSTDDLKTEEEGKTDGEGNPDDGAK

Ligands and cofactors

ID	Name	Formula	Copies
1PW	(2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate	C20 H40 N O6 P	1
LPE	1-O-octadecyl-sn-glycero-3-phosphocholine	C26 H57 N O6 P	17
CLR	Cholesterol	C27 H46 O	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	5
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7
P5S	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine	C42 H82 N O10 P	1
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	6

Primary citation

Unwinding and spiral sliding of S4 and domain rotation of VSD during the electromechanical coupling in Na v 1.7. Huang, G., Wu, Q., Li, Z. et al. Proc Natl Acad Sci U S A (2022) 119:e2209164119-e2209164119. DOI 10.1073/pnas.2209164119 · 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
8G1A 2.8 Å, Cryo-EM structure of Nav1.7 with CBD

Browse structure collections

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