9IXY: PDB entry 9IXY

Human KCNQ2-CaM-Ebio2 Complex in the Presence of PIP2. Determined by electron microscopy at 3.1 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 8
Atoms: 16,132
Mol. weight: 366.31 kDa
Ligands: PIO, A1L3C
Released: 19 Mar 2025

Explore 9IXY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IXY contains 92 α-helices and 16 β-strands across 8 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.

Chains A, B, C and D: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	72-85	14
α-helix	91-114	24
α-helix	119-147	29
α-helix	156-163	8
α-helix	167-183	17
α-helix	196-209	14
α-helix	216-227	12
α-helix	229-254	26
α-helix	264-275	12
α-helix	288-347	60
α-helix	357-366	10
α-helix	537-558	22
α-helix	564-599	36

Chains E, F, G and H: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	27-29	3	1
α-helix	30-39	10
α-helix	46-54	9
β-strand	63-65	3	1
α-helix	66-74	9
α-helix	77-80	4
α-helix	83-91	9
β-strand	100-102	3	2
α-helix	103-112	10
α-helix	116-118	3
α-helix	119-129	11
β-strand	136-138	3	2
α-helix	139-147	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 3 of Potassium voltage-gated channel subfamily KQT member 2	A, B, C, D	protein	628	Homo sapiens	O43526 (AlphaFold model)
Calmodulin-3	E, F, G, H	protein	177	Homo sapiens	P0DP25 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9IXY_1 Isoform 3 of Potassium voltage-gated channel subfamily KQT member 2 (chains A, B, C, D)
MAGKPPKRNAFYRKLQNFLYNVLERPRGWAFIYHAYVFLLVFSCLVLSVFSTIKEYEKSS
EGALYILEIVTIVVFGVEYFVRIWAAGCCCRYRGWRGRLKFARKPFCVIDIMVLIASIAV
LAAGSQGNVFATSALRSLRFLQILRMIRMDRRGGTWKLLGSVVYAHSKELVTAWYIGFLC
LILASFLVYLAEKGENDHFDTYADALWWGLITLTTIGYGDKYPQTWNGRLLAATFTLIGV
SFFALPAGILGSGFALKVQEQHRQKHFEKRRNPAAGLIQSAWRFYATNLSRTDLHSTWQY
YERTVTVPMYRLIPPLNQLELLRNLKSKSGLAFRKDPPPEPSPSQKVSLKDRVFSSPRGV
AAKGKGSPQAQTVRRSPSADQSLEDSPSKVPKSWSFGDRSRARQAFRIKGAASRQNSEEA
SLPGEDIVDDKSCPCEFVTEDLTPGLKVSIRAVCVMRFLVSKRKFKESLRPYDVMDVIEQ
YSAGHLDMLSRIKSLQSRVDQIVGRGPAITDKDRTKGPAEAELPEDPSMMGRLGKVEKQV
LSMEKKLDFLVNIYMQRMGIPPTETEAYFGAKEPEPAPPYHSPEDSREHVDRHGCIVKIV
RSSSSTGQKNFSLEGGSSGGWSHPQFEK

Sequence of entity 2 (E, F, G, H), FASTA

>9IXY_2 Calmodulin-3 (chains E, F, G, H)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAKLEGGSSGGLVPRGSGGSSGGHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PIO	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-d…	C25 H49 O19 P3	4
A1L3C	~{N}-[7-[bis(fluoranyl)methoxy]-1-prop-2-ynyl-indazol-3-yl]-3,3-dimethyl-butana…	C17 H19 F2 N3 O2	4

Primary citation

Small molecule inhibits KCNQ channels with a non-blocking mechanism. Li, J., Yang, Z., Zhang, S. et al. Nat Chem Biol (2025) 21:1100-1109. DOI 10.1038/s41589-024-01834-8 · PubMed

Other PDB entries of the same protein (UniProt O43526 (AlphaFold model), which also has an AlphaFold model), best resolution first:

22AY 2.3 Å, KCNQ2 homotetramer in apo state
22BJ 2.4 Å, KCNQ2/3 heterotetramer with 3:1 stoichiometry
22BF 2.5 Å, XEN1101 bound KCNQ2/3 heteromer with 3:1 stoichiometry, state 2
22BG 2.5 Å, XEN1101 bound KCNQ2/3 heteromer with 3:1 stoichiometry, state 3
8IZY 2.5 Å, Human KCNQ2-CaM in complex with HN37
22BE 2.6 Å, XEN1101 bound KCNQ2/3 heteromer with 3:1 stoichiometry, state 1
22BI 2.6 Å, XEN1101 bound KCNQ2/3 heteromer with 2:2 stoichiometry
22AZ 2.7 Å, ICA-1103811 bound KCNQ2/3 heteromer with 3:1 stoichiometry, state 1
22BK 2.7 Å, KCNQ2/3 heterotetramer with 2:2 stoichiometry
8J03 2.7 Å, Human KCNQ2(F104A)-CaM-PIP2-CBD complex in state I
8J04 2.7 Å, Human KCNQ2-CaM-HN37 complex in the presence of PIP2
8J05 2.7 Å, Human KCNQ2-CaM complex in the presence of PIP2

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