9ED1: Human KCa3.1/calmodulin channel

Cryo-EM structure of the human KCa3.1/calmodulin channel in complex with Ca2+ and 1,4-dihydropyridine (DHP-103). Determined by electron microscopy at 3.5 Å resolution. Released 16 Apr 2025.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Homo sapiens, Rattus norvegicus
Chains: 8
Atoms: 15,449
Mol. weight: 236.69 kDa
Ligands: CA
Released: 16 Apr 2025

Explore 9ED1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ED1 contains 111 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.

Chain A: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	15-18	4
α-helix	31-37	7
α-helix	40-45	6
α-helix	58-91	34
α-helix	96-99	4
α-helix	104-114	11
α-helix	150-154	5
α-helix	155-161	7
α-helix	162-168	7
α-helix	177-183	7
α-helix	192-202	11
α-helix	204-222	19
α-helix	224-227	4
α-helix	237-240	4
α-helix	243-248	6
α-helix	263-288	26
α-helix	293-331	39
α-helix	337-368	32
α-helix	373-384	12

Chain B: 19 helices, 0 β-strands

Element	Residues	Length
α-helix	32-49	18
α-helix	58-70	13
α-helix	73-90	18
α-helix	96-99	4
α-helix	104-114	11
α-helix	145-146	2
α-helix	150-154	5
α-helix	155-161	7
α-helix	162-170	9
α-helix	191-202	12
α-helix	204-222	19
α-helix	224-227	4
α-helix	237-240	4
α-helix	243-248	6
α-helix	263-288	26
α-helix	293-314	22
α-helix	316-331	16
α-helix	337-368	32
α-helix	372-384	13

Chain C: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	32-35	4
α-helix	37-49	13
α-helix	60-90	31
α-helix	96-99	4
α-helix	104-114	11
α-helix	149-154	6
α-helix	155-162	8
α-helix	163-170	8
α-helix	177-183	7
α-helix	192-202	11
α-helix	204-222	19
α-helix	224-227	4
α-helix	237-240	4
α-helix	243-248	6
α-helix	261-263	3
α-helix	266-288	23
α-helix	293-302	10
α-helix	304-331	28
α-helix	337-368	32
α-helix	373-384	12

Chain D: 22 helices, 0 β-strands

Element	Residues	Length
α-helix	28-49	22
α-helix	58-70	13
α-helix	73-90	18
α-helix	96-99	4
α-helix	104-114	11
α-helix	145-146	2
α-helix	150-154	5
α-helix	155-162	8
α-helix	163-169	7
α-helix	177-183	7
α-helix	192-202	11
α-helix	204-218	15
α-helix	224-227	4
α-helix	237-240	4
α-helix	243-248	6
α-helix	266-285	20
α-helix	291-292	2
α-helix	293-314	22
α-helix	319-331	13
α-helix	337-367	31
α-helix	368-371	4
α-helix	373-382	10

Chain E: 7 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	8-19	12
β-strand	27	1	1
α-helix	29-38	10
α-helix	45-50	6
β-strand	63	1	1
α-helix	66-75	10
β-strand	100	1	2
α-helix	102-111	10
α-helix	118-128	11
β-strand	136	1	2
α-helix	138-146	9

Chain F: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
β-strand	27	1	3
α-helix	29-38	10
α-helix	45-55	11
β-strand	63	1	3
α-helix	66-75	10
α-helix	83-86	4
β-strand	100	1	4
α-helix	102-111	10
α-helix	118-128	11
β-strand	136	1	4
α-helix	138-146	9

Chain G: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-20	15
β-strand	27	1	5
α-helix	29-38	10
α-helix	45-53	9
β-strand	63	1	5
α-helix	65-72	8
α-helix	83-86	4
β-strand	100	1	6
α-helix	102-111	10
α-helix	118-128	11
β-strand	136	1	6
α-helix	138-146	9

Chain H: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
β-strand	27	1	7
α-helix	31-38	8
α-helix	45-55	11
β-strand	63	1	7
α-helix	66-75	10
α-helix	83-86	4
β-strand	100	1	8
α-helix	102-111	10
α-helix	118-128	11
β-strand	136	1	8
α-helix	138-145	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Intermediate conductance calcium-activated potassium channel protein 4	A, B, C, D	protein	378	Homo sapiens	O15554 (AlphaFold model)
Calmodulin-1	E, F, G, H	protein	145	Rattus norvegicus	P0DP29 (AlphaFold model)

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

>9ED1_1 Intermediate conductance calcium-activated potassium channel protein 4 (chains A, B, C, D)
LGALRRRKRLLEQEKSLAGWALVLAGTGIGLMVLHAEMLWFGGCSWALYLFLVKCTISIS
TFLLLCLIVAFHAKEVQLFMTDNGLRDWRVALTGRQAAQIVLELVVCGLHPAPVRGPPCV
QDLGAPLTSPQPWPGFLGQGEALLSLAMLLRLYLVPRAVLLRSGVLLNASYRSIGALNQV
RFRHWFVAKLYMNTHPGRLLLGLTLGLWLTTAWVLSVAERQAVNATGHLSDTLWLIPITF
LTIGYGDVVPGTMWGKIVCLCTGVMGVCCTALLVAVVARKLEFNKAEKHVHNFMMDIQYT
KEMKESAARVLQEAWMFYKHTRRKESHAARRHQRKLLAAINAFRQVRLKHRKLREQVNSM
VDISKMHMILYDLQQNLS

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

>9ED1_2 Calmodulin-1 (chains E, F, G, H)
QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGT
IDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVD
EMIREADIDGDGQVNYEEFVQMMTA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	12

Water and common crystallization additives (K) are not listed.

Primary citation

Design and structural basis of selective 1,4-dihydropyridine inhibitors of the calcium-activated potassium channel K Ca 3.1. Ong, S.T., Nam, Y.W., Nasburg, J.A. et al. Proc Natl Acad Sci U S A (2025) 122:e2425494122-e2425494122. DOI 10.1073/pnas.2425494122 · PubMed

Other PDB entries of the same protein (UniProt O15554 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6D42 1.75 Å, Crystal structure of the KCa3.1 C-terminal four-helix bundle (with copper)
9ZRK 2.99 Å, Cryo-EM structure of KCa3.1_I/calmodulin channel in complex with SKA111.
9O48 3.1 Å, Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex in the Ca2+…
9O5O 3.1 Å, Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex bound to a small…
9O52 3.18 Å, Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex bound to the bee…
9O53 3.3 Å, Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex bound to a small…
9ZRL 3.38 Å, Cryo-EM structure of KCa3.1_II/calmodulin channel in complex with SKA111.
9ZPT 3.39 Å, Cryo-EM structure of KCa3.1_II/calmodulin channel in complex with SKA31.
6CNM 3.4 Å, Cryo-EM structure of the human SK4/calmodulin channel complex
9O51 3.4 Å, Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex in the Ca2+ free…
9YDZ 3.4 Å, Cryo EM structure of KCa3.1_R355K_II/calmodulin channel in complex with rimtuzalcap
6CNN 3.5 Å, Cryo-EM structure of the human SK4/calmodulin channel complex in the Ca2+ bound state I

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