8J04: PDB entry 8J04

Human KCNQ2-CaM-HN37 complex in the presence of PIP2. Determined by electron microscopy at 2.7 Å resolution. Released 6 Dec 2023.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 8
Atoms: 15,580
Mol. weight: 375.7 kDa
Ligands: 9MF
Released: 6 Dec 2023

Explore 8J04 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8J04 contains 104 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, D and G: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	71-85	15
α-helix	92-113	22
α-helix	119-147	29
α-helix	148-150	3
α-helix	152-154	3
α-helix	156-164	9
α-helix	167-183	17
α-helix	197-209	13
α-helix	216-227	12
α-helix	229-254	26
α-helix	264-275	12
α-helix	288-328	41
α-helix	333-349	17
α-helix	358-365	8
α-helix	536-557	22
α-helix	564-577	14

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

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	27-28	2	1
α-helix	30-40	11
α-helix	46-56	11
β-strand	64-65	2	1
α-helix	66-74	9
α-helix	77-79	3
α-helix	83-93	11
β-strand	101-102	2	2
α-helix	103-110	8
α-helix	119-129	11
β-strand	136-137	2	2
α-helix	139-142	4
α-helix	143-147	5

Chain H: 10 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	28	1	7
α-helix	30-40	11
α-helix	46-56	11
β-strand	64	1	7
α-helix	66-74	9
α-helix	77-79	3
α-helix	83-93	11
β-strand	101-102	2	8
α-helix	103-110	8
α-helix	119-129	11
β-strand	136-137	2	8
α-helix	139-142	4
α-helix	143-147	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Potassium voltage-gated channel subfamily KQT member 2	A, B, D, G	protein	656	Homo sapiens	O43526 (AlphaFold model)
Calmodulin-1	C, E, F, H	protein	177	Homo sapiens	P0DP23 (AlphaFold model)

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

>8J04_1 Potassium voltage-gated channel subfamily KQT member 2 (chains A, B, D, G)
MAGKPPKRNAFYRKLQNFLYNVLERPRGWAFIYHAYVFLLVFSCLVLSVFSTIKEYEKSS
EGALYILEIVTIVVFGVEYFVRIWAAGCCCRYRGWRGRLKFARKPFCVIDIMVLIASIAV
LAAGSQGNVFATSALRSLRFLQILRMIRMDRRGGTWKLLGSVVYAHSKELVTAWYIGFLC
LILASFLVYLAEKGENDHFDTYADALWWGLITLTTIGYGDKYPQTWNGRLLAATFTLIGV
SFFALPAGILGSGFALKVQEQHRQKHFEKRRNPAAGLIQSAWRFYATNLSRTDLHSTWQY
YERTVTVPMYSSQTQTYGASRLIPPLNQLELLRNLKSKSGLAFRKDPPPEPSPSKGSPCR
GPLCGCCPGRSSQKVSLKDRVFSSPRGVAAKGKGSPQAQTVRRSPSADQSLEDSPSKVPK
SWSFGDRSRARQAFRIKGAASRQNSEEASLPGEDIVDDKSCPCEFVTEDLTPGLKVSIRA
VCVMRFLVSKRKFKESLRPYDVMDVIEQYSAGHLDMLSRIKSLQSRVDQIVGRGPAITDK
DRTKGPAEAELPEDPSMMGRLGKVEKQVLSMEKKLDFLVNIYMQRMGIPPTETEAYFGAK
EPEPAPPYHSPEDSREHVDRHGCIVKIVRSSSSTGQKNFSVEGGSSGGWSHPQFEK

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

>8J04_2 Calmodulin-1 (chains C, E, F, H)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAKLEGGSSGGLVPRGSGGSSGGHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
9MF	methyl N-[4-[(4-fluorophenyl)methyl-prop-2-ynyl-amino]-2,6-dimethyl-phenyl]carb…	C20 H21 F N2 O2	8

Primary citation

Ligand activation mechanisms of human KCNQ2 channel. Ma, D., Zheng, Y., Li, X. et al. Nat Commun (2023) 14:6632-6632. DOI 10.1038/s41467-023-42416-x · 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
8J05 2.7 Å, Human KCNQ2-CaM complex in the presence of PIP2
22BC 2.8 Å, ICA-1103811 bound KCNQ2/3 heteromer with 3:1 stoichiometry, state 3

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