9XB9: Human KCNQ2-CaM

Human KCNQ2-CaM in complex with QO-58 and PIP2. Determined by electron microscopy at 3.1 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 8
Atoms: 16,520
Mol. weight: 456.08 kDa
Ligands: A1LVR, PIO
Released: 28 Jan 2026

Explore 9XB9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XB9 contains 96 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: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	71-86	16
α-helix	91-114	24
α-helix	116-147	32
α-helix	148-150	3
α-helix	156-164	9
α-helix	167-186	20
α-helix	194-209	16
α-helix	216-227	12
α-helix	229-253	25
α-helix	259-261	3
α-helix	264-275	12
α-helix	288-348	61
α-helix	357-365	9
α-helix	536-558	23
α-helix	564-599	36

Chains E, F, G and H: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	27-28	2	1
α-helix	30-38	9
α-helix	46-55	10
β-strand	64-65	2	1
α-helix	66-74	9
α-helix	79-81	3
α-helix	82-91	10
β-strand	100-102	3	2
α-helix	103-107	5
α-helix	119-129	11
β-strand	136-138	3	2
α-helix	140-147	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Potassium voltage-gated channel subfamily KQT member 2	A, B, C, D	protein	872	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

>9XB9_1 Potassium voltage-gated channel subfamily KQT member 2 (chains A, B, C, D)
MVQKSRNGGVYPGPSGEKKLKVGFVGLDPGAPDSTRDGALLIAGSEAPKRGSILSKPRAG
GAGAGKPPKRNAFYRKLQNFLYNVLERPRGWAFIYHAYVFLLVFSCLVLSVFSTIKEYEK
SSEGALYILEIVTIVVFGVEYFVRIWAAGCCCRYRGWRGRLKFARKPFCVIDIMVLIASI
AVLAAGSQGNVFATSALRSLRFLQILRMIRMDRRGGTWKLLGSVVYAHSKELVTAWYIGF
LCLILASFLVYLAEKGENDHFDTYADALWWGLITLTTIGYGDKYPQTWNGRLLAATFTLI
GVSFFALPAGILGSGFALKVQEQHRQKHFEKRRNPAAGLIQSAWRFYATNLSRTDLHSTW
QYYERTVTVPMYSSQTQTYGASRLIPPLNQLELLRNLKSKSGLAFRKDPPPEPSPSKGSP
CRGPLCGCCPGRSSQKVSLKDRVFSSPRGVAAKGKGSPQAQTVRRSPSADQSLEDSPSKV
PKSWSFGDRSRARQAFRIKGAASRQNSEEASLPGEDIVDDKSCPCEFVTEDLTPGLKVSI
RAVCVMRFLVSKRKFKESLRPYDVMDVIEQYSAGHLDMLSRIKSLQSRVDQIVGRGPAIT
DKDRTKGPAEAELPEDPSMMGRLGKVEKQVLSMEKKLDFLVNIYMQRMGIPPTETEAYFG
AKEPEPAPPYHSPEDSREHVDRHGCIVKIVRSSSSTGQKNFSAPPAAPPVQCPPSTSWQP
QSHPRQGHGTSPVGDHGSLVRIPPPPAHERSLSAYGGGNRASMEFLRQEDTPGCRPPEGN
LRDSDTSISIPSVDHEELERSFSGFSISQSKENLDALNSCYAAVAPCAKVRPYIAEGESD
TDSDLCTPCGPPPRSATGEGPFGDVGWAGPRK

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

>9XB9_2 Calmodulin-1 (chains E, F, G, H)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
A1LVR	QO-58	C18 H8 Cl2 F4 N4 O	4
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

Primary citation

Structure basis for the activation of KCNQ2 by endogenous and exogenous ligands. Zhao, Y., Yang, Z., Shi, S. et al. Cell Rep (2025) 45:116771-116771. DOI 10.1016/j.celrep.2025.116771 · 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

Browse structure collections

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