9Y5Q: PDB entry 9Y5Q
Cryo EM structure of KCa3.1_R355K_I/calmodulin channel in complex with rimtuzalcap. Determined by electron microscopy at 4.73 Å resolution. Released 15 Oct 2025.
- Method
- Electron microscopy
- Resolution
- 4.73 Å
- Organism
- Homo sapiens
- Chains
- 8
- Atoms
- 15,135
- Mol. weight
- 238.08 kDa
- Ligands
- CA, A1B92
- Released
- 15 Oct 2025
Explore 9Y5Q in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9Y5Q contains 100 α-helices and 0 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: 16 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-49 | 40 | |
| α-helix | 58-91 | 34 | |
| α-helix | 96-99 | 4 | |
| α-helix | 102-116 | 15 | |
| α-helix | 151-155 | 5 | |
| α-helix | 156-158 | 3 | |
| α-helix | 162-170 | 9 | |
| α-helix | 177-184 | 8 | |
| α-helix | 194-202 | 9 | |
| α-helix | 204-223 | 20 | |
| α-helix | 243-248 | 6 | |
| α-helix | 261-278 | 18 | |
| α-helix | 283-288 | 6 | |
| α-helix | 293-330 | 38 | |
| α-helix | 336-366 | 31 | |
| α-helix | 370-384 | 15 | |
Chain B: 18 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-43 | 34 | |
| α-helix | 52-54 | 3 | |
| α-helix | 57-90 | 34 | |
| α-helix | 96-99 | 4 | |
| α-helix | 102-116 | 15 | |
| α-helix | 151-154 | 4 | |
| α-helix | 155-161 | 7 | |
| α-helix | 162-169 | 8 | |
| α-helix | 177-183 | 7 | |
| α-helix | 194-202 | 9 | |
| α-helix | 206-223 | 18 | |
| α-helix | 237-240 | 4 | |
| α-helix | 243-248 | 6 | |
| α-helix | 263-278 | 16 | |
| α-helix | 282-289 | 8 | |
| α-helix | 293-330 | 38 | |
| α-helix | 335-366 | 32 | |
| α-helix | 370-384 | 15 | |
Chain C: 18 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-39 | 30 | |
| α-helix | 43-48 | 6 | |
| α-helix | 55-90 | 36 | |
| α-helix | 102-116 | 15 | |
| α-helix | 151-154 | 4 | |
| α-helix | 155-161 | 7 | |
| α-helix | 162-170 | 9 | |
| α-helix | 172-174 | 3 | |
| α-helix | 177-184 | 8 | |
| α-helix | 194-202 | 9 | |
| α-helix | 206-226 | 21 | |
| α-helix | 237-240 | 4 | |
| α-helix | 261-277 | 17 | |
| α-helix | 282-288 | 7 | |
| α-helix | 293-330 | 38 | |
| α-helix | 335-337 | 3 | |
| α-helix | 338-368 | 31 | |
| α-helix | 371-384 | 14 | |
Chain D: 16 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-48 | 39 | |
| α-helix | 57-90 | 34 | |
| α-helix | 104-116 | 13 | |
| α-helix | 147-154 | 8 | |
| α-helix | 155-161 | 7 | |
| α-helix | 162-170 | 9 | |
| α-helix | 177-184 | 8 | |
| α-helix | 194-202 | 9 | |
| α-helix | 208-224 | 17 | |
| α-helix | 237-248 | 12 | |
| α-helix | 261-278 | 18 | |
| α-helix | 282-285 | 4 | |
| α-helix | 293-330 | 38 | |
| α-helix | 335-347 | 13 | |
| α-helix | 350-367 | 18 | |
| α-helix | 371-384 | 14 | |
Chains E and G: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-19 | 14 | |
| α-helix | 29-38 | 10 | |
| α-helix | 45-55 | 11 | |
| α-helix | 65-73 | 9 | |
| α-helix | 85-89 | 5 | |
| α-helix | 102-109 | 8 | |
| α-helix | 120-128 | 9 | |
| α-helix | 138-145 | 8 | |
Chain F: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-19 | 14 | |
| α-helix | 29-39 | 11 | |
| α-helix | 45-55 | 11 | |
| α-helix | 65-73 | 9 | |
| α-helix | 87-90 | 4 | |
| α-helix | 102-109 | 8 | |
| α-helix | 120-128 | 9 | |
| α-helix | 138-145 | 8 | |
Chain H: 8 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-19 | 14 | |
| α-helix | 29-38 | 10 | |
| α-helix | 45-55 | 11 | |
| α-helix | 65-73 | 9 | |
| α-helix | 85-89 | 5 | |
| α-helix | 102-109 | 8 | |
| α-helix | 120-128 | 9 | |
| α-helix | 138-146 | 9 | |
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 | 146 | Homo sapiens | P0DP23 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D), FASTA
>9Y5Q_1 Intermediate conductance calcium-activated potassium channel protein 4 (chains A, B, C, D)
LGALRRRKRLLEQEKSLAGWALVLAGTGIGLMVLHAEMLWFGGCSWALYLFLVKCTISIS
TFLLLCLIVAFHAKEVQLFMTDNGLRDWRVALTGRQAAQIVLELVVCGLHPAPVRGPPCV
QDLGAPLTSPQPWPGFLGQGEALLSLAMLLRLYLVPRAVLLRSGVLLNASYRSIGALNQV
RFRHWFVAKLYMNTHPGRLLLGLTLGLWLTTAWVLSVAERQAVNATGHLSDTLWLIPITF
LTIGYGDVVPGTMWGKIVCLCTGVMGVCCTALLVAVVARKLEFNKAEKHVHNFMMDIQYT
KEMKESAARVLQEAWMFYKHTRRKESHAARRHQRKLLAAINAFRQVKLKHRKLREQVNSM
VDISKMHMILYDLQQNLS
Sequence of entity 2 (E, F, G, H), FASTA
>9Y5Q_2 Calmodulin-1 (chains E, F, G, H)
DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNG
TIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEV
DEMIREADIDGDGQVNYEEFVQMMTA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 4 |
| A1B92 | Rimtuzalcap | C18 H24 F2 N6 O | 4 |
Water and common crystallization additives (K) are not listed.
Primary citation
Structural basis for the subtype-selectivity of K Ca 2.2 channel activators. Nam, Y.W., Ramanishka, A., Xu, Y. et al. Nat Commun (2026) 17:531-531. DOI 10.1038/s41467-025-67232-3 · 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
Browse structure collections
About this viewer
MolViewer shows 9Y5Q directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.