8X43: PDB entry 8X43

human KCNQ2-CaM-Ebio1-S1 complex in the presence of PIP2. Determined by electron microscopy at 3.0 Å resolution. Released 17 Jan 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 8
Atoms: 15,180
Mol. weight: 363.15 kDa
Ligands: 7Q0
Released: 17 Jan 2024

Explore 8X43 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X43 contains 88 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, E and G: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	71-85	15
α-helix	92-114	23
α-helix	119-147	29
α-helix	148-150	3
α-helix	156-164	9
α-helix	167-181	15
α-helix	196-210	15
α-helix	216-227	12
α-helix	229-254	26
α-helix	264-275	12
α-helix	288-329	42
α-helix	333-349	17
α-helix	539-559	21
α-helix	564-594	31

Chains B and H: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	28	1	1
α-helix	30-40	11
α-helix	46-56	11
β-strand	64	1	1
α-helix	66-74	9
α-helix	83-93	11
β-strand	100-101	2	2
α-helix	103-112	10
α-helix	119-129	11
β-strand	137-138	2	2
α-helix	140-147	8

Chains D and F: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	28	1	3
α-helix	30-40	11
α-helix	46-56	11
β-strand	64	1	3
α-helix	66-73	8
α-helix	83-93	11
β-strand	100-101	2	4
α-helix	103-112	10
α-helix	119-129	11
β-strand	137-138	2	4
α-helix	140-147	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Potassium voltage-gated channel subfamily KQT member 2	A, C, E, G	protein	656	Homo sapiens	O43526 (AlphaFold model)
Calmodulin-1	B, D, F, H	protein	149	Homo sapiens	P0DP23 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>8X43_1 Potassium voltage-gated channel subfamily KQT member 2 (chains A, C, E, G)
MAGKPPKRNAFYRKLQNFLYNVLERPRGWAFIYHAYVFLLVFSCLVLSVFSTIKEYEKSS
EGALYILEIVTIVVFGVEYFVRIWAAGCCCRYRGWRGRLKFARKPFCVIDIMVLIASIAV
LAAGSQGNVFATSALRSLRFLQILRMIRMDRRGGTWKLLGSVVYAHSKELVTAWYIGFLC
LILASFLVYLAEKGENDHFDTYADALWWGLITLTTIGYGDKYPQTWNGRLLAATFTLIGV
SFFALPAGILGSGFALKVQEQHRQKHFEKRRNPAAGLIQSAWRFYATNLSRTDLHSTWQY
YERTVTVPMYSSQTQTYGASRLIPPLNQLELLRNLKSKSGLAFRKDPPPEPSPSKGSPCR
GPLCGCCPGRSSQKVSLKDRVFSSPRGVAAKGKGSPQAQTVRRSPSADQSLEDSPSKVPK
SWSFGDRSRARQAFRIKGAASRQNSEEASLPGEDIVDDKSCPCEFVTEDLTPGLKVSIRA
VCVMRFLVSKRKFKESLRPYDVMDVIEQYSAGHLDMLSRIKSLQSRVDQIVGRGPAITDK
DRTKGPAEAELPEDPSMMGRLGKVEKQVLSMEKKLDFLVNIYMQRMGIPPTETEAYFGAK
EPEPAPPYHSPEDSREHVDRHGCIVKIVRSSSSTGQKNFSVEGGSSGGWSHPQFEK

Sequence of entity 2 (B, D, F, H), FASTA

>8X43_2 Calmodulin-1 (chains B, D, F, H)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
7Q0	N-(4-azanyl-1,2-dihydroacenaphthylen-5-yl)-4-fluoranyl-benzamide	C19 H15 F N2 O	4

Primary citation

A small-molecule activation mechanism that directly opens the KCNQ2 channel. Zhang, S., Ma, D., Wang, K. et al. Nat Chem Biol (2024) 20:847-856. DOI 10.1038/s41589-023-01515-y · 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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