6J8E: Human Nav1.2-beta2-KIIIA ternary complex

Human Nav1.2-beta2-KIIIA ternary complex. Determined by electron microscopy at 3.0 Å resolution. Released 27 Feb 2019.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Conus kinoshitai
Chains: 3
Atoms: 10,482
Mol. weight: 251.19 kDa
Ligands: 9Z9, NAG
Released: 27 Feb 2019

Explore 6J8E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J8E contains 68 α-helices and 22 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	118-121	4
α-helix	124-127	4
α-helix	129-145	17
α-helix	156-174	19
α-helix	190-202	13
α-helix	204-206	3
α-helix	218-224	7
α-helix	227-230	4
α-helix	234-245	12
α-helix	246-249	4
α-helix	251-269	19
α-helix	273-275	3
β-strand	276-280	5	4
α-helix	281-282	2
β-strand	342	1	5
β-strand	344	1	5
β-strand	351-355	5	4
α-helix	370-381	12
α-helix	386-396	11
α-helix	399-401	3
α-helix	402-408	7
α-helix	409-414	6
α-helix	415-440	26
α-helix	742-753	12
α-helix	763-777	15
α-helix	788-807	20
α-helix	823-840	18
α-helix	847-862	16
α-helix	865-878	14
α-helix	882-902	21
α-helix	904-909	6
α-helix	928-938	11
α-helix	944-954	11
α-helix	956-985	30
α-helix	1195-1205	11
α-helix	1208-1223	16
α-helix	1224-1227	4
α-helix	1232-1235	4
α-helix	1239-1264	26
α-helix	1266-1269	4
α-helix	1273-1294	22
α-helix	1302-1305	4
α-helix	1306-1316	11
α-helix	1321-1330	10
α-helix	1331-1333	3
α-helix	1334-1358	25
β-strand	1365-1368	4	6
β-strand	1373-1374	2	6
α-helix	1375-1376	2
β-strand	1382	1	7
α-helix	1383-1390	8
β-strand	1397-1399	3	6
α-helix	1409-1420	12
α-helix	1424-1432	9
β-strand	1439	1	7
α-helix	1447-1449	3
α-helix	1450-1457	8
α-helix	1458-1463	6
α-helix	1464-1482	19
α-helix	1492-1496	5
α-helix	1501-1505	5
α-helix	1520-1528	9
α-helix	1531-1549	19
α-helix	1557-1584	28
α-helix	1593-1615	23
α-helix	1622-1628	7
α-helix	1629-1633	5
α-helix	1636-1641	6
α-helix	1646-1654	9
α-helix	1657-1681	25
α-helix	1700-1710	11
α-helix	1716-1720	5
α-helix	1749-1784	36

Chain C: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	1
β-strand	37-41	5	2
β-strand	46-48	3	3
β-strand	51-52	2	1
β-strand	64-70	7	2
β-strand	77-84	8	2
β-strand	86-89	4	2
β-strand	99-101	3	3
β-strand	104	1	1
α-helix	105-107	3
β-strand	109	1	1
β-strand	112-114	3	3
α-helix	119-121	3
β-strand	123-130	8	2
α-helix	136-137	2
β-strand	138-147	10	2

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sodium channel subunit beta-2	C	protein	122	Homo sapiens	O60939 (AlphaFold model)
Sodium channel protein type 2 subunit alpha	A	protein	2048	Homo sapiens	Q99250 (AlphaFold model)
Mu-conotoxin KIIIA	D	protein	16	Conus kinoshitai	P0C195 (AlphaFold model)

Sequence of entity 1 (C), FASTA

>6J8E_1 Sodium channel subunit beta-2 (chains C)
GRSMEVTVPATLNVLNGSDARLPCTFNSCYTVNHKQFSLNWTYQECNNCSEEMFLQFRMK
IINLKLERFQDRVEFSGNPSKYDVSVMLRNVQPEDEGIYNCYIMNPPDRHRGHGKIHLQV
LM

Sequence of entity 2 (A), FASTA

>6J8E_2 Sodium channel protein type 2 subunit alpha (chains A)
MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTMAQSVLVPPGPDSFRFF
TRESLAAIEQRIAEEKAKRPKQERKDEDDENGPKPNSDLEAGKSLPFIYGDIPPEMVSVP
LEDLDPYYINKKTFIVLNKGKAISRFSATPALYILTPFNPIRKLAIKILVHSLFNMLIMC
TILTNCVFMTMSNPPDWTKNVEYTFTGIYTFESLIKILARGFCLEDFTFLRDPWNWLDFT
VITFAYVTEFVDLGNVSALRTFRVLRALKTISVIPGLKTIVGALIQSVKKLSDVMILTVF
CLSVFALIGLQLFMGNLRNKCLQWPPDNSSFEINITSFFNNSLDGNGTTFNRTVSIFNWD
EYIEDKSHFYFLEGQNDALLCGNSSDAGQCPEGYICVKAGRNPNYGYTSFDTFSWAFLSL
FRLMTQDFWENLYQLTLRAAGKTYMIFFVLVIFLGSFYLINLILAVVAMAYEEQNQATLE
EAEQKEAEFQQMLEQLKKQQEEAQAAAAAASAESRDFSGAGGIGVFSESSSVASKLSSKS
EKELKNRRKKKKQKEQSGEEEKNDRVRKSESEDSIRRKGFRFSLEGSRLTYEKRFSSPHQ
SLLSIRGSLFSPRRNSRASLFSFRGRAKDIGSENDFADDEHSTFEDNDSRRDSLFVPHRH
GERRHSNVSQASRASRVLPILPMNGKMHSAVDCNGVVSLVGGPSTLTSAGQLLPEGTTTE
TEIRKRRSSSYHVSMDLLEDPTSRQRAMSIASILTNTMEELEESRQKCPPCWYKFANMCL
IWDCCKPWLKVKHLVNLVVMDPFVDLAITICIVLNTLFMAMEHYPMTEQFSSVLSVGNLV
FTGIFTAEMFLKIIAMDPYYYFQEGWNIFDGFIVSLSLMELGLANVEGLSVLRSFRLLRV
FKLAKSWPTLNMLIKIIGNSVGALGNLTLVLAIIVFIFAVVGMQLFGKSYKECVCKISND
CELPRWHMHDFFHSFLIVFRVLCGEWIETMWDCMEVAGQTMCLTVFMMVMVIGNLVVLNL
FLALLLSSFSSDNLAATDDDNEMNNLQIAVGRMQKGIDFVKRKIREFIQKAFVRKQKALD
EIKPLEDLNNKKDSCISNHTTIEIGKDLNYLKDGNGTTSGIGSSVEKYVVDESDYMSFIN
NPSLTVTVPIAVGESDFENLNTEEFSSESDMEESKEKLNATSSSEGSTVDIGAPAEGEQP
EVEPEESLEPEACFTEDCVRKFKCCQISIEEGKGKLWWNLRKTCYKIVEHNWFETFIVFM
ILLSSGALAFEDIYIEQRKTIKTMLEYADKVFTYIFILEMLLKWVAYGFQVYFTNAWCWL
DFLIVDVSLVSLTANALGYSELGAIKSLRTLRALRPLRALSRFEGMRVVVNALLGAIPSI
MNVLLVCLIFWLIFSIMGVNLFAGKFYHCINYTTGEMFDVSVVNNYSECKALIESNQTAR
WKNVKVNFDNVGLGYLSLLQVATFKGWMDIMYAAVDSRNVELQPKYEDNLYMYLYFVIFI
IFGSFFTLNLFIGVIIDNFNQQKKKFGGQDIFMTEEQKKYYNAMKKLGSKKPQKPIPRPA
NKFQGMVFDFVTKQVFDISIMILICLNMVTMMVETDDQSQEMTNILYWINLVFIVLFTGE
CVLKLISLRYYYFTIGWNIFDFVVVILSIVGMFLAELIEKYFVSPTLFRVIRLARIGRIL
RLIKGAKGIRTLLFALMMSLPALFNIGLLLFLVMFIYAIFGMSNFAYVKREVGIDDMFNF
ETFGNSMICLFQITTSAGWDGLLAPILNSGPPDCDPDKDHPGSSVKGDCGNPSVGIFFFV
SYIIISFLVVVNMYIAVILENFSVATEESAEPLSEDDFEMFYEVWEKFDPDATQFIEFAK
LSDFADALDPPLLIAKPNKVQLIAMDLPMVSGDRIHCLDILFAFTKRVLGESGEMDALRI
QMEERFMASNPSKVSYEPITTTLKRKQEEVSAIIIQRAYRRYLLKQKVKKVSSIYKKDKG
KECDGTPIKEDTLIDKLNENSTPEKTDMTPSTTSPPSYDSVTKPEKEKFEKDKSEKEDKG
KDIRESKK

Sequence of entity 3 (D), FASTA

>6J8E_3 Mu-conotoxin KIIIA (chains D)
CCNCSSKWCRDHSRCC

Ligands and cofactors

ID	Name	Formula	Copies
9Z9	(3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en	C34 H56 O5	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Molecular basis for pore blockade of human Na+channel Nav1.2 by the mu-conotoxin KIIIA. Pan, X., Li, Z., Huang, X. et al. Science (2019) 363:1309-1313. DOI 10.1126/science.aaw2999 · PubMed

Other PDB entries of the same protein (UniProt O60939 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5FEB 1.35 Å, Crystal structure of the Voltage-gated Sodium Channel Beta 2 subunit extracellular domain
6VRR 1.45 Å, Crystal structure of a disease mutant of the Voltage-gated Sodium Channel Beta 2 subunit…
5FDY 1.85 Å, Crystal structure of the Voltage-gated Sodium Channel Beta 2 subunit extracellular…
7W9K 2.2 Å, Cryo-EM structure of human Nav1.7-beta1-beta2 complex at 2.2 angstrom resolution
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
8G1A 2.8 Å, Cryo-EM structure of Nav1.7 with CBD

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6J8E is part of these collections:

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