9O52: Human SK2-4 chimera/calmodulin channel complex
Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex bound to the bee toxin apamin. Determined by electron microscopy at 3.18 Å resolution. Released 9 Jul 2025.
- Method
- Electron microscopy
- Resolution
- 3.18 Å
- Organisms
- Homo sapiens, Apis mellifera
- Chains
- 9
- Atoms
- 16,185
- Mol. weight
- 267.77 kDa
- Ligands
- CA
- Released
- 9 Jul 2025
Explore 9O52 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9O52 contains 100 α-helices and 26 β-strands across 9 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: 16 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 119-156 | 38 | |
| α-helix | 165-199 | 35 | |
| α-helix | 205-208 | 4 | |
| α-helix | 211-224 | 14 | |
| β-strand | 234-240 | 7 | 1 |
| β-strand | 247-253 | 7 | 1 |
| α-helix | 260-266 | 7 | |
| α-helix | 267-275 | 9 | |
| α-helix | 278-280 | 3 | |
| α-helix | 283-291 | 9 | |
| α-helix | 298-308 | 11 | |
| α-helix | 310-332 | 23 | |
| α-helix | 345-356 | 12 | |
| α-helix | 369-395 | 27 | |
| α-helix | 399-400 | 2 | |
| α-helix | 401-438 | 38 | |
| α-helix | 442-476 | 35 | |
| α-helix | 479-489 | 11 | |
Chain B: 16 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 119-156 | 38 | |
| α-helix | 167-199 | 33 | |
| α-helix | 205-208 | 4 | |
| α-helix | 211-224 | 14 | |
| β-strand | 234-241 | 8 | 2 |
| β-strand | 246-253 | 8 | 2 |
| α-helix | 254-256 | 3 | |
| α-helix | 260-266 | 7 | |
| α-helix | 267-275 | 9 | |
| 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 | 371-395 | 25 | |
| α-helix | 401-438 | 38 | |
| α-helix | 442-476 | 35 | |
| α-helix | 479-489 | 11 | |
Chain C: 18 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 119-158 | 40 | |
| α-helix | 165-168 | 4 | |
| α-helix | 171-199 | 29 | |
| α-helix | 205-208 | 4 | |
| α-helix | 211-224 | 14 | |
| β-strand | 234 | 1 | 3 |
| β-strand | 237-240 | 4 | 4 |
| α-helix | 241 | 1 | |
| β-strand | 247-250 | 4 | 4 |
| β-strand | 253 | 1 | 3 |
| α-helix | 254-256 | 3 | |
| α-helix | 260-266 | 7 | |
| α-helix | 267-275 | 9 | |
| α-helix | 278-280 | 3 | |
| α-helix | 283-291 | 9 | |
| α-helix | 298-308 | 11 | |
| α-helix | 310-333 | 24 | |
| α-helix | 345-351 | 7 | |
| α-helix | 371-396 | 26 | |
| α-helix | 403-438 | 36 | |
| α-helix | 442-476 | 35 | |
| α-helix | 478-489 | 12 | |
Chain D: 17 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 119-158 | 40 | |
| α-helix | 165-168 | 4 | |
| α-helix | 171-199 | 29 | |
| α-helix | 205-208 | 4 | |
| α-helix | 211-224 | 14 | |
| β-strand | 234-240 | 7 | 5 |
| β-strand | 247-253 | 7 | 5 |
| α-helix | 256-259 | 4 | |
| α-helix | 260-266 | 7 | |
| α-helix | 267-275 | 9 | |
| α-helix | 278-280 | 3 | |
| α-helix | 283-291 | 9 | |
| α-helix | 298-308 | 11 | |
| α-helix | 310-332 | 23 | |
| α-helix | 345-356 | 12 | |
| α-helix | 369-396 | 28 | |
| α-helix | 403-438 | 36 | |
| α-helix | 442-476 | 35 | |
| α-helix | 479-489 | 11 | |
Chains E, F, G and H: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-20 | 14 | |
| β-strand | 28 | 1 | 6 |
| α-helix | 30-39 | 10 | |
| α-helix | 46-53 | 8 | |
| β-strand | 64 | 1 | 6 |
| α-helix | 66-76 | 11 | |
| α-helix | 82-93 | 12 | |
| β-strand | 101 | 1 | 7 |
| α-helix | 103-108 | 6 | |
| α-helix | 120-129 | 10 | |
| β-strand | 137 | 1 | 7 |
| α-helix | 139-146 | 8 | |
Chain I: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 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) |
| Apamin | I | protein | 18 | Apis mellifera | P01500 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D), FASTA
>9O52_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
>9O52_2 Calmodulin-1 (chains E, F, G, H)
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVQMMTAK
Sequence of entity 3 (I), FASTA
>9O52_3 Apamin (chains I)
CNCKAPETALCARRCQQH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 16 |
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…
- 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
- 9ED1 3.5 Å, Cryo-EM structure of the human KCa3.1/calmodulin channel in complex with Ca2+ and…
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