SMTL ID : 6cnn.1

Cryo-EM structure of the human SK4/calmodulin channel complex in the Ca2+ bound state I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.50 Å

Oligo State

hetero-4-4-mer

Ligands

4 x K: POTASSIUM ION(Non-covalent)

K.1: 9 residues within 4Å: Chain A: G.252, Y.253 Chain B: G.252, Y.253 Chain C: G.252, Y.253 Chain D: G.252, Y.253 Ligands: K.2 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 2 interactions with chain A, 1 interactions with chain B Metal complexes: D:Y.253, C:Y.253, A:G.252, A:Y.253, B:Y.253 K.2: 10 residues within 4Å: Chain A: I.251, G.252 Chain B: I.251, G.252 Chain C: I.251, G.252 Chain D: I.251, G.252 Ligands: K.1, K.3 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C, 1 interactions with chain A Metal complexes: B:I.251, B:G.252, D:G.252, C:G.252, A:G.252 K.3: 10 residues within 4Å: Chain A: T.250, I.251 Chain B: T.250, I.251 Chain C: T.250, I.251 Chain D: T.250, I.251 Ligands: K.2, K.4 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Metal complexes: D:T.250, D:I.251, B:I.251, A:I.251, C:I.251 K.4: 5 residues within 4Å: Chain A: T.250 Chain B: T.250 Chain C: T.250 Chain D: T.250 Ligands: K.3 No protein-ligand interaction detected (PLIP)

4 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.5: 4 residues within 4Å: Chain D: F.49, H.236, S.238, L.241 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.241 Salt bridges: D:H.236 POV.8: 5 residues within 4Å: Chain A: F.49, L.217, H.236, S.238, L.241 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.217, A:L.241 Salt bridges: A:H.236 POV.11: 5 residues within 4Å: Chain B: F.49, L.217, H.236, S.238, L.241 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.217, B:L.241 Salt bridges: B:H.236 POV.14: 5 residues within 4Å: Chain C: F.49, L.217, H.236, S.238, L.241 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.217, C:L.241 Salt bridges: C:H.236

8 x LMT: DODECYL-BETA-D-MALTOSIDE(Covalent)(Non-covalent)

LMT.6: 8 residues within 4Å: Chain A: G.259, M.261, K.264, I.265, L.268 Chain D: W.216, S.238, L.241 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:K.264, A:I.265, A:L.268, D:W.216 Hydrogen bonds: A:G.259 Salt bridges: A:K.264 LMT.7: 9 residues within 4Å: Chain A: F.144, L.145, G.146, A.150, L.154, A.226, W.262, I.265, V.266 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.154, A:A.226, A:W.262, A:W.262, A:W.262, A:I.265, A:V.266 Hydrogen bonds: A:L.145 LMT.9: 8 residues within 4Å: Chain A: W.216, S.238, L.241 Chain B: G.259, M.261, K.264, I.265, L.268 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.264, B:I.265, B:L.268, A:W.216 Hydrogen bonds: B:G.259 Salt bridges: B:K.264 LMT.10: 9 residues within 4Å: Chain B: F.144, L.145, G.146, A.150, L.154, A.226, W.262, I.265, V.266 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.154, B:A.226, B:W.262, B:W.262, B:W.262, B:I.265, B:V.266 Hydrogen bonds: B:L.145 LMT.12: 8 residues within 4Å: Chain B: W.216, S.238, L.241 Chain C: G.259, M.261, K.264, I.265, L.268 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:W.216, C:K.264, C:I.265, C:L.268 Hydrogen bonds: C:G.259 Salt bridges: C:K.264 LMT.13: 9 residues within 4Å: Chain C: F.144, L.145, G.146, A.150, L.154, A.226, W.262, I.265, V.266 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.154, C:A.226, C:W.262, C:W.262, C:W.262, C:I.265, C:V.266 Hydrogen bonds: C:L.145 LMT.15: 8 residues within 4Å: Chain C: W.216, S.238, L.241 Chain D: G.259, M.261, K.264, I.265, L.268 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:K.264, D:I.265, D:L.268, C:W.216 Hydrogen bonds: D:G.259 Salt bridges: D:K.264 LMT.16: 9 residues within 4Å: Chain D: F.144, L.145, G.146, A.150, L.154, A.226, W.262, I.265, V.266 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.154, D:A.226, D:W.262, D:W.262, D:W.262, D:I.265, D:V.266 Hydrogen bonds: D:L.145

12 x CA: CALCIUM ION(Non-covalent)

CA.17: 5 residues within 4Å: Chain E: D.21, D.23, D.25, T.27, E.32 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.21, E:D.23, E:D.25, E:T.27, E:E.32 CA.18: 5 residues within 4Å: Chain E: D.57, D.59, N.61, T.63, E.68 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.57, E:D.59, E:T.63, E:E.68, E:E.68 CA.19: 6 residues within 4Å: Chain E: D.94, D.96, N.98, Y.100, I.101, E.105 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.94, E:D.96, E:Y.100, E:E.105, E:E.105 CA.20: 5 residues within 4Å: Chain F: D.21, D.23, D.25, T.27, E.32 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.21, F:D.23, F:D.25, F:T.27, F:E.32 CA.21: 5 residues within 4Å: Chain F: D.57, D.59, N.61, T.63, E.68 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.57, F:D.59, F:T.63, F:E.68, F:E.68 CA.22: 6 residues within 4Å: Chain F: D.94, D.96, N.98, Y.100, I.101, E.105 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.94, F:D.96, F:Y.100, F:E.105, F:E.105 CA.23: 5 residues within 4Å: Chain G: D.21, D.23, D.25, T.27, E.32 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.21, G:D.23, G:D.25, G:T.27, G:E.32 CA.24: 5 residues within 4Å: Chain G: D.57, D.59, N.61, T.63, E.68 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.57, G:D.59, G:T.63, G:E.68, G:E.68 CA.25: 6 residues within 4Å: Chain G: D.94, D.96, N.98, Y.100, I.101, E.105 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.94, G:D.96, G:Y.100, G:E.105, G:E.105 CA.26: 5 residues within 4Å: Chain H: D.21, D.23, D.25, T.27, E.32 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.21, H:D.23, H:D.25, H:T.27, H:E.32 CA.27: 5 residues within 4Å: Chain H: D.57, D.59, N.61, T.63, E.68 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.57, H:D.59, H:T.63, H:E.68, H:E.68 CA.28: 6 residues within 4Å: Chain H: D.94, D.96, N.98, Y.100, I.101, E.105 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.94, H:D.96, H:Y.100, H:E.105, H:E.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, C.H. et al., Activation mechanism of a human SK-calmodulin channel complex elucidated by cryo-EM structures. Science (2018)

Release Date

2018-05-02

Peptides

Intermediate conductance calcium-activated potassium channel protein 4: ABCD
Calmodulin-1: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Membrane

We predict this structure to be a membrane protein.
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Intermediate conductance calcium-activated potassium channel protein 4

Calmodulin-1

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