7XMF: Human NaV1.7/beta1/beta2-Nav1.7-IN2

Cryo-EM structure of human NaV1.7/beta1/beta2-Nav1.7-IN2. Determined by electron microscopy at 3.07 Å resolution. Released 30 Nov 2022.

Method: Electron microscopy
Resolution: 3.07 Å
Organisms: Homo sapiens, Aequorea victoria
Chains: 3
Atoms: 11,709
Mol. weight: 337.09 kDa
Ligands: G2W, NAG
Released: 30 Nov 2022

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

Secondary structure: helices and β-sheets

7XMF contains 76 α-helices and 32 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: 69 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	115-123	9
α-helix	126-143	18
α-helix	152-174	23
α-helix	181-184	4
α-helix	189-203	15
α-helix	210-214	5
α-helix	215-218	4
α-helix	219-227	9
α-helix	231-267	37
α-helix	270-272	3
β-strand	273-277	5	1
α-helix	286-290	5
α-helix	296-300	5
β-strand	303	1	1
α-helix	312-314	3
α-helix	324-325	2
β-strand	328-332	5	1
α-helix	335-336	2
α-helix	338-340	3
α-helix	347-358	12
α-helix	363-374	12
α-helix	376-378	3
α-helix	379-384	6
α-helix	385-393	9
α-helix	394-416	23
α-helix	727-740	14
α-helix	746-761	16
α-helix	770-798	29
α-helix	801-804	4
α-helix	807-820	14
α-helix	835-846	12
α-helix	850-862	13
α-helix	867-894	28
α-helix	896-898	3
α-helix	913-924	12
α-helix	929-939	11
α-helix	941-950	10
α-helix	951-955	5
α-helix	956-971	16
α-helix	1177-1190	14
α-helix	1192-1207	16
α-helix	1214-1216	3
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	2
β-strand	1357	1	2
β-strand	1366	1	3
α-helix	1367-1376	10
β-strand	1380-1383	4	2
α-helix	1392-1404	13
α-helix	1408-1417	10
β-strand	1423	1	3
α-helix	1424-1426	3
α-helix	1434-1440	7
α-helix	1441-1448	8
α-helix	1449-1466	18
α-helix	1476-1486	11
α-helix	1487-1489	3
α-helix	1492-1495	4
α-helix	1498-1500	3
α-helix	1503-1513	11
α-helix	1515-1533	19
α-helix	1541-1568	28
α-helix	1573-1575	3
α-helix	1577-1602	26
α-helix	1606-1613	8
α-helix	1614-1616	3
α-helix	1617-1621	5
α-helix	1622-1625	4
α-helix	1628-1665	38
α-helix	1684-1695	12
α-helix	1700-1704	5
α-helix	1733-1767	35

Chain B: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
α-helix	30	1
β-strand	31	1	4
β-strand	36-38	3	5
β-strand	54-61	8	6
β-strand	68-73	6	6
β-strand	78-80	3	6
β-strand	90-92	3	5
β-strand	106-108	3	5
β-strand	117-124	8	6
β-strand	126	1	7
β-strand	135	1	7
β-strand	138-144	7	6
β-strand	147	1	4
α-helix	150-153	4
α-helix	154-190	37

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	8
β-strand	37-40	4	9
β-strand	46-48	3	10
β-strand	51-53	3	8
β-strand	64-70	7	9
β-strand	78-84	7	9
β-strand	87-89	3	9
α-helix	93-95	3
β-strand	99-101	3	10
α-helix	105-107	3
β-strand	109	1	8
β-strand	112-114	3	10
α-helix	119-121	3
β-strand	123-130	8	9
β-strand	137-146	10	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 3 of Sodium channel protein type 9 subunit alpha,Green fluorescent protein	A	protein	2250	Homo sapiens, Aequorea victoria	Q15858 (AlphaFold model)
Sodium channel subunit beta-1,Green fluorescent protein	B	protein	481	Homo sapiens, Aequorea victoria	Q07699 (AlphaFold model)
Sodium channel subunit beta-2	C	protein	215	Homo sapiens	O60939 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7XMF_1 Isoform 3 of Sodium channel protein type 9 subunit alpha,Green fluorescent protein (chains A)
MAMLPPPGPQSFVHFTKQSLALIEQRIAERKSKEPKEEKKDDDEEAPKPSSDLEAGKQLP
FIYGDIPPGMVSEPLEDLDPYYADKKTFIVLNKGKTIFRFNATPALYMLSPFSPLRRISI
KILVHSLFSMLIMCTILTNCIFMTMNNPPDWTKNVEYTFTGIYTFESLVKILARGFCVGE
FTFLRDPWNWLDFVVIVFAYLTEFVNLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQ
SVKKLSDVMILTVFCLSVFALIGLQLFMGNLKHKCFRNSLENNETLESIMNTLESEEDFR
KYFYYLEGSKDALLCGFSTDSGQCPEGYTCVKIGRNPDYGYTSFDTFSWAFLALFRLMTQ
DYWENLYQQTLRAAGKTYMIFFVVVIFLGSFYLINLILAVVAMAYEEQNQANIEEAKQKE
LEFQQMLDRLKKEQEEAEAIAAAAAEYTSIRRSRIMGLSESSSETSKLSSKSAKERRNRR
KKKNQKKLSSGEEKGDAEKLSKSESEDSIRRKSFHLGVEGHRRAHEKRLSTPNQSPLSIR
GSLFSARRSSRTSLFSFKGRGRDIGSETEFADDEHSIFGDNESRRGSLFVPHRPQERRSS
NISQASRSPPMLPVNGKMHSAVDCNGVVSLVDGRSALMLPNGQLLPEGTTNQIHKKRRCS
SYLLSEDMLNDPNLRQRAMSRASILTNTVEELEESRQKCPPWWYRFAHKFLIWNCSPYWI
KFKKCIYFIVMDPFVDLAITICIVLNTLFMAMEHHPMTEEFKNVLAIGNLVFTGIFAAEM
VLKLIAMDPYEYFQVGWNIFDSLIVTLSLVELFLADVEGLSVLRSFRLLRVFKLAKSWPT
LNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKINDDCTLPRWHMN
DFFHSFLIVFRVLCGEWIETMWDCMEVAGQAMCLIVYMMVMVIGNLVVLNLFLALLLSSF
SSDNLTAIEEDPDANNLQIAVTRIKKGINYVKQTLREFILKAFSKKPKISREIRQAEDLN
TKKENYISNHTLAEMSKGHNFLKEKDKISGFGSSVDKHLMEDSDGQSFIHNPSLTVTVPI
APGESDLENMNAEELSSDSDSEYSKVRLNRSSSSECSTVDNPLPGEGEEAEAEPMNSDEP
EACFTDGCVRRFSCCQVNIESGKGKIWWNIRKTCYKIVEHSWFESFIVLMILLSSGALAF
EDIYIERKKTIKIILEYADKIFTYIFILEMLLKWIAYGYKTYFTNAWCWLDFLIVDVSLV
TLVANTLGYSDLGPIKSLRTLRALRPLRALSRFEGMRVVVNALIGAIPSIMNVLLVCLIF
WLIFSIMGVNLFAGKFYECINTTDGSRFPASQVPNRSECFALMNVSQNVRWKNLKVNFDN
VGLGYLSLLQVATFKGWTIIMYAAVDSVNVDKQPKYEYSLYMYIYFVVFIIFGSFFTLNL
FIGVIIDNFNQQKKKLGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPGNKIQGCIFDL
VTNQAFDISIMVLICLNMVTMMVEKEGQSQHMTEVLYWINVVFIILFTGECVLKLISLRH
YYFTVGWNIFDFVVVIISIVGMFLADLIETYFVSPTLFRVIRLARIGRILRLVKGAKGIR
TLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKKEDGINDMFNFETFGNSMICL
FQITTSAGWDGLLAPILNSKPPDCDPKKVHPGSSVEGDCGNPSVGIFYFVSYIIISFLVV
VNMYIAVILENFSVATEESTEPLSEDDFEMFYEVWEKFDPDATQFIEFSKLSDFAAALDP
PLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGESGEMDSLRSQMEERFMSAN
PSKVSYEPITTTLKRKQEDVSATVIQRAYRRYRLRQNVKNISSIYIKDGDRDDDLLNKKD
MAFDNVNENSSPEKTDATSSTTSPPSYDSVTKPDKEKYEQDRTEKEDKGKDSKESKKAAA
LEVLFQGPSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKL
PVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVK
FEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVED
GSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGM
DEWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Sequence of entity 2 (B), FASTA

>7XMF_2 Sodium channel subunit beta-1,Green fluorescent protein (chains B)
MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAEAAALEVLFQGPSKGEELFTGVV
PILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFS
RYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKE
DGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGP
VLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGMDEHHHHHHHHHHDYKDDDD
K

Sequence of entity 3 (C), FASTA

>7XMF_3 Sodium channel subunit beta-2 (chains C)
MHRDAWLPRPAFSLTGLSLFFSLVPPGRSMEVTVPATLNVLNGSDARLPCTFNSCYTVNH
KQFSLNWTYQECNNCSEEMFLQFRMKIINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPE
DEGIYNCYIMNPPDRHRGHGKIHLQVLMEEPPERDSTVAVIVGASVGGFLAVVILVLMVV
KCVRRKKEQKLSTDDLKTEEEGKTDGEGNPDDGAK

Ligands and cofactors

ID	Name	Formula	Copies
G2W	3-[[4-[3-(4-fluoranyl-2-methyl-phenoxy)azetidin-1-yl]pyrimidin-2-yl]amino]-~{N}…	C22 H22 F N5 O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Structural basis for Na V 1.7 inhibition by pore blockers. Zhang, J., Shi, Y., Huang, Z. et al. Nat Struct Mol Biol (2022) 29:1208-1216. DOI 10.1038/s41594-022-00860-1 · 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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