9O53: Human SK2-4 chimera/calmodulin channel complex

Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex bound to a small molecule inhibitor. Determined by electron microscopy at 3.3 Å resolution. Released 9 Jul 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 8
Atoms: 15,628
Mol. weight: 267.43 kDa
Ligands: CA, A1B8D
Released: 9 Jul 2025

Explore 9O53 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9O53 contains 99 α-helices and 24 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: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	121-158	38
α-helix	165-200	36
α-helix	205-207	3
α-helix	211-224	14
β-strand	234-240	7	1
β-strand	247-253	7	1
α-helix	256-259	4
α-helix	260-266	7
α-helix	267-276	10
α-helix	278-281	4
α-helix	283-291	9
α-helix	298-308	11
α-helix	310-319	10
α-helix	321-333	13
α-helix	334-336	3
α-helix	345-356	12
α-helix	369-397	29
α-helix	399-400	2
α-helix	401-438	38
α-helix	443-476	34

Chain B: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	121-158	38
α-helix	165-200	36
α-helix	205-208	4
α-helix	211-223	13
β-strand	234-240	7	2
β-strand	247-253	7	2
α-helix	256-259	4
α-helix	260-266	7
α-helix	267-276	10
α-helix	278-281	4
α-helix	283-291	9
α-helix	298-308	11
α-helix	310-333	24
α-helix	334-336	3
α-helix	345-356	12
α-helix	369-397	29
α-helix	399-400	2
α-helix	401-438	38
α-helix	443-476	34

Chains C and D: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	121-158	38
α-helix	165-200	36
α-helix	205-208	4
α-helix	211-223	13
β-strand	234-240	7	3
β-strand	247-253	7	3
α-helix	256-259	4
α-helix	260-266	7
α-helix	267-276	10
α-helix	278-281	4
α-helix	283-291	9
α-helix	298-308	11
α-helix	310-333	24
α-helix	345-356	12
α-helix	369-397	29
α-helix	399-400	2
α-helix	401-438	38
α-helix	443-476	34

Chain E: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	28	1	5
α-helix	30-39	10
α-helix	46-53	8
β-strand	64	1	5
α-helix	66-76	11
α-helix	82-93	12
β-strand	101	1	6
α-helix	103-110	8
α-helix	120-129	10
β-strand	137	1	6
α-helix	139-146	8

Chains F, G and H: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
β-strand	28	1	7
α-helix	30-39	10
α-helix	46-53	8
β-strand	64	1	7
α-helix	66-76	11
α-helix	82-93	12
β-strand	101	1	8
α-helix	103-109	7
α-helix	120-129	10
β-strand	137	1	8
α-helix	139-146	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Intermediate conductance calcium-activated potassium channel protein 4,Small conductance…	A, B, C, D	protein	435	Homo sapiens	O15554 (AlphaFold model), Q9H2S1 (AlphaFold model)
Calmodulin-1	E, F, G, H	protein	149	Homo sapiens	P0DP23 (AlphaFold model)

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

>9O53_1 Intermediate conductance calcium-activated potassium channel protein 4,Small conductance calcium-activated potassium channel protein 2 chimera (chains A, B, C, D)
MGGDLVLGLGALRRRRALFEKRKRLSDYALIFGMFGIVVMVIETELSWGAYDKASLYSLA
LKCLISLSTIILLGLIIVYHAREIQLFMVDNGADDWRIAMTYERIFFICLEILVCAIHPI
PGNYTFTWTARLAFSYAPSTTTADVDIILSIPMFLRLYLIARVMLLHSKLFTDASSRSIG
ALNKINFNTRFVMKTLMTICPGTVLLVFSISLWIIAAWTVRACERYHDQQDVTSNFLGAM
WLISITFLSIGYGDMVPNTYCGKGVCLLTGIMGAGCTALVVAVVARKLELTKAEKHVHNF
MMDIQYTKEMKESAARVLQEAWMFYKHTRRKESHAARRHQRKLLAAINAFRQVRLKHRKL
REQVNSMVDISKMHMILYDLQQNLSSSHRALEKQIDTLAGKLDALTELLSTALGPRQLPE
PSQQSKSSSLEVLFQ

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

>9O53_2 Calmodulin-1 (chains E, F, G, H)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	16
A1B8D	N-(2,1,3-benzoxadiazol-4-yl)-3-(4-methoxybenzene-1-sulfonamido)benzamide	C20 H16 N4 O5 S	4

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

Primary citation

Mechanism of SK2 channel gating and its modulation by the bee toxin apamin and small molecules. Cassell, S.J., Li, W., Krautwald, S. et al. Elife (2025) 14. DOI 10.7554/eLife.107733 · 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…
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
9ED1 3.5 Å, Cryo-EM structure of the human KCa3.1/calmodulin channel in complex with Ca2+ and…

Browse structure collections

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