8XMM: Voltage-gated sodium channel Nav1.7 variant M9

Voltage-gated sodium channel Nav1.7 variant M9. Determined by electron microscopy at 2.89 Å resolution. Released 6 Mar 2024.

Method: Electron microscopy
Resolution: 2.89 Å
Organism: Homo sapiens
Chains: 2
Atoms: 11,389
Mol. weight: 271.02 kDa
Ligands: LPE, 1PW, PCW, P5S
Released: 6 Mar 2024

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

Secondary structure: helices and β-sheets

8XMM contains 72 α-helices and 21 β-strands across 2 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: 70 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	115-123	9
α-helix	126-142	17
α-helix	152-174	23
α-helix	187-204	18
α-helix	210-215	6
α-helix	216-223	8
α-helix	224-227	4
α-helix	229-244	16
α-helix	246-266	21
α-helix	270-272	3
β-strand	273-276	4	1
α-helix	286-292	7
α-helix	296-302	7
β-strand	303	1	1
α-helix	312-314	3
β-strand	329-332	4	1
α-helix	335-336	2
α-helix	338-340	3
β-strand	346	1	2
α-helix	347-359	13
α-helix	363-373	11
α-helix	376-378	3
α-helix	379-384	6
α-helix	385-390	6
α-helix	391-416	26
α-helix	727-741	15
α-helix	744-761	18
α-helix	770-796	27
α-helix	800-803	4
α-helix	807-824	18
α-helix	826-827	2
α-helix	832-836	5
α-helix	837-847	11
α-helix	850-861	12
α-helix	863-888	26
α-helix	891-894	4
α-helix	897-899	3
α-helix	913-924	12
α-helix	930-939	10
α-helix	941-952	12
α-helix	953-959	7
α-helix	960-970	11
α-helix	1176-1190	15
α-helix	1192-1210	19
α-helix	1220-1248	29
α-helix	1250-1254	5
α-helix	1257-1277	21
α-helix	1284-1289	6
α-helix	1291-1300	10
α-helix	1305-1315	11
α-helix	1318-1343	26
β-strand	1349-1352	4	3
β-strand	1357-1358	2	3
β-strand	1366	1	4
α-helix	1367-1376	10
β-strand	1380-1383	4	3
α-helix	1392-1404	13
α-helix	1408-1415	8
β-strand	1423	1	4
α-helix	1431-1433	3
α-helix	1434-1440	7
α-helix	1441-1448	8
α-helix	1449-1467	19
α-helix	1476-1488	13
α-helix	1491-1500	10
α-helix	1505-1513	9
α-helix	1515-1533	19
β-strand	1536	1	2
α-helix	1541-1569	29
α-helix	1577-1601	25
α-helix	1606-1613	8
α-helix	1614-1616	3
α-helix	1617-1620	4
α-helix	1621-1626	6
α-helix	1628-1665	38
α-helix	1684-1695	12
α-helix	1700-1708	9
α-helix	1733-1747	15
α-helix	1748-1753	6
α-helix	1754-1767	14

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
β-strand	29-31	3	5
β-strand	36-38	3	6
β-strand	50-51	2	7
β-strand	54-61	8	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	117-128	12	7
β-strand	133-144	12	7
β-strand	145-147	3	5
α-helix	154-191	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium channel protein type 9 subunit alpha	A	protein	2031	Homo sapiens	Q15858 (AlphaFold model)
Sodium channel subunit beta-1	B	protein	230	Homo sapiens	Q07699 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8XMM_1 Sodium channel protein type 9 subunit alpha (chains A)
MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMAMLPPPGPQSFVHFTK
QSLALIEQRIAERKSKEPKEEKKDDDEEAPKPSSDLEAGKQLPFIYGDIPPGMVSEPLED
LDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRISIKILVHSLFSMLIMCTIL
TNCIFMTMNNPPDWTKNVEYTFTGIYTFESLVKILARGFCVGEFTFLRDPWNWLDFVVIV
FAYLTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMILTVFCLS
VFALIGLQLFMGNLKHKCFRNSLENNETLESIMNTLESEEDFRKYFYYLEGSKDALLCGF
STDSGQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQDYWENLYQQTLRAAGKT
YMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQKELEFQQMLDRLKKEQEEA
EAIAAAAAEYTSIRRSRIMGLSESSSETSKLSSKSAKERRNRRKKKNQKKLSSGEEKGDA
EKLSKSESEDSIRRKSFHLGVEGHRRAHEKRLSTPNQSPLSIRGSLFSARRSSRTSLFSF
KGRGRDIGSETEFADDEHSIFGDNESRRGSLFVPHRPQERRSSNISQASRSPPMLPVNGK
MHSAVDCNGVVSLVDGRSALMLPNGQLLPEVIIDKATSDDSGTTNQIHKKRRCSSYLLSE
DMLNDPNLRQRAMSRASILTNTVEELEESRQKCPPWWYRFAHKFLIWNCSPYWIKFKKCI
YFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGNLVFTGIFAAEMVLKLIA
MDPYEYFQVGWNIFDSLIVTLSLVELFLADVEGLSVLRSFRLLRVFKLAKSWPTLNMLIK
IIGNSVGAFGNLMLVLFIIVFIFAVVGMQLFGKSYKECVCKINDDCTLPRWHMNDFFHSF
LIVFRVLCGEWIETMWDCMEVAGQAMCLIFYMMVFFIGNLVVLNLFLALLLSSFSSDNLT
AIEEDPDANNLQIAVTRIKKGINYVKQTLREFILKAFSKKPKISREIRQAEDLNTKKENY
ISNHTLAEMSKGHNFLKEKDKISGFGSSVDKHLMEDSDGQSFIHNPSLTVTVPIAPGESD
LENMNAEELSSDSDSEYSKVRLNRSSSSECSTVDNPLPGEGEEAEAEPMNSDEPEACFTD
GCVWRFSCCQVNIESGKGKIWWNIRKTCYKIVEHSWFESFIVLMILLSSGALAFEDIYIE
RKKTIKIILEYADKIFTYIFILEMLLKWIAYGYKTYFTNAWCWLDFLIVDVSLVTLVANT
LGYSDLGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIFWLIFSI
MGVNLFAGKFYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDNVGLGYL
SLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFIFFIIFGSFFTLNLFICVII
DNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPGNKIQGCIFDLVTNQAF
DISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRHYYFTVG
WNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIRTLLFAL
MMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICLFQITTS
AGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYIIISFLVVVNMYIA
VILENFSVATEESTEPLSEDDFEMFYEVWEKFDPDATQFIEFSKLSDFAAALDPPLLIAK
PNKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGESGEMDSLRSQMEERFMSANPSKVSY
EPITTTLKRKQEDVSATVIQRAYRRYRLRQNVKNISSIYIKDGDRDDDLLNKKDMAFDNV
NENSSPEKTDATSSTTSPPSYDSVTKPDKEKYEQDRTEKEDKGKDSKESKK

Sequence of entity 2 (B), FASTA

>8XMM_2 Sodium channel subunit beta-1 (chains B)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAELEHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
LPE	1-O-octadecyl-sn-glycero-3-phosphocholine	C26 H57 N O6 P	9
1PW	(2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate	C20 H40 N O6 P	1
PCW	1,2-dioleoyl-sn-glycero-3-phosphocholine	C44 H85 N O8 P	6
P5S	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine	C42 H82 N O10 P	1
CLR	Cholesterol	C27 H46 O	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Dissection of the structure-function relationship of Na v channels. Li, Z., Wu, Q., Huang, G. et al. Proc Natl Acad Sci U S A (2024) 121:e2322899121-e2322899121. DOI 10.1073/pnas.2322899121 · 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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