9IXZ: PDB entry 9IXZ

human KCNQ2-CaM-Ebio3 Complex in the Presence of PIP2. Determined by electron microscopy at 3.2 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 8
Atoms: 16,292
Mol. weight: 345.11 kDa
Ligands: A1L3D
Released: 19 Mar 2025

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

Secondary structure: helices and β-sheets

9IXZ contains 100 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, C and D: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	71-86	16
α-helix	92-114	23
α-helix	119-150	32
α-helix	152-154	3
α-helix	156-164	9
α-helix	167-188	22
α-helix	193-210	18
α-helix	216-227	12
α-helix	229-254	26
α-helix	264-275	12
α-helix	288-329	42
α-helix	334-348	15
α-helix	357-365	9
α-helix	537-558	22
α-helix	563-594	32

Chain B: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	71-86	16
α-helix	92-114	23
α-helix	119-150	32
α-helix	152-154	3
α-helix	156-164	9
α-helix	167-188	22
α-helix	193-210	18
α-helix	216-227	12
α-helix	229-254	26
α-helix	264-275	12
α-helix	288-329	42
α-helix	334-347	14
α-helix	357-365	9
α-helix	537-558	22
α-helix	563-594	32

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

Element	Residues	Length	Sheet
α-helix	1007-1020	14
β-strand	1027-1028	2	1
α-helix	1030-1039	10
α-helix	1046-1056	11
β-strand	1064-1065	2	1
α-helix	1066-1074	9
α-helix	1077-1080	4
α-helix	1083-1093	11
β-strand	1100-1102	3	2
α-helix	1103-1105	3
α-helix	1106-1110	5
α-helix	1119-1129	11
β-strand	1136-1138	3	2
α-helix	1139-1147	9

Chain F: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	1007-1020	14
β-strand	1027-1028	2	3
α-helix	1030-1039	10
α-helix	1046-1056	11
β-strand	1064-1065	2	3
α-helix	1066-1073	8
α-helix	1077-1080	4
α-helix	1083-1093	11
β-strand	1100-1102	3	4
α-helix	1103-1105	3
α-helix	1106-1110	5
α-helix	1119-1129	11
β-strand	1136-1138	3	4
α-helix	1139-1147	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	611	Homo sapiens	O43526 (AlphaFold model)
Calmodulin-1	E, F, G, H	protein	149	Homo sapiens	P0DP23 (AlphaFold model)

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

>9IXZ_1 Isoform 3 of Potassium voltage-gated channel subfamily KQT member 2 (chains A, B, C, D)
AGKPPKRNAFYRKLQNFLYNVLERPRGWAFIYHAYVFLLVFSCLVLSVFSTIKEYEKSSE
GALYILEIVTIVVFGVEYFVRIWAAGCCCRYRGWRGRLKFARKPFCVIDIMVLIASIAVL
AAGSQGNVFATSALRSLRFLQILRMIRMDRRGGTWKLLGSVVYAHSKELVTAWYIGFLCL
ILASFLVYLAEKGENDHFDTYADALWWGLITLTTIGYGDKYPQTWNGRLLAATFTLIGVS
FFALPAGILGSGFALKVQEQHRQKHFEKRRNPAAGLIQSAWRFYATNLSRTDLHSTWQYY
ERTVTVPMYRLIPPLNQLELLRNLKSKSGLAFRKDPPPEPSPSQKVSLKDRVFSSPRGVA
AKGKGSPQAQTVRRSPSADQSLEDSPSKVPKSWSFGDRSRARQAFRIKGAASRQNSEEAS
LPGEDIVDDKSCPCEFVTEDLTPGLKVSIRAVCVMRFLVSKRKFKESLRPYDVMDVIEQY
SAGHLDMLSRIKSLQSRVDQIVGRGPAITDKDRTKGPAEAELPEDPSMMGRLGKVEKQVL
SMEKKLDFLVNIYMQRMGIPPTETEAYFGAKEPEPAPPYHSPEDSREHVDRHGCIVKIVR
SSSSTGQKNFS

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

>9IXZ_2 Calmodulin-1 (chains E, F, G, H)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
A1L3D	~{N}-[7-[bis(fluoranyl)methoxy]-1-prop-2-ynyl-indazol-3-yl]-2-propyl-pentanamide	C19 H23 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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