SMTL ID : 6cnm.1

Cryo-EM structure of the human SK4/calmodulin channel complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

hetero-4-4-mer

Ligands

5 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

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 A, 2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Metal complexes: A:Y.253, D:G.252, D:Y.253, C: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: 1 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain D Metal complexes: C:G.252, A:G.252, B:I.251, B:G.252, D: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:T.250, A:T.250, C:T.250 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) K.5: 0 residues within 4Å: (No contacts) 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.6: 1 residues within 4Å: Chain D: H.236 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.238 Salt bridges: D:H.236 POV.9: 2 residues within 4Å: Chain A: H.236, S.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.238 Salt bridges: A:H.236 POV.12: 2 residues within 4Å: Chain B: H.236, S.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.238 Salt bridges: B:H.236 POV.15: 1 residues within 4Å: Chain C: H.236 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.238 Salt bridges: C:H.236

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

LMT.7: 7 residues within 4Å: Chain A: G.259, M.261, K.264, I.265, L.268 Chain D: S.238, L.241 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.264, A:I.265, A:L.268 Hydrogen bonds: A:G.259 Salt bridges: A:K.264 LMT.8: 9 residues within 4Å: Chain A: F.144, G.146, Q.147, A.150, L.154, V.225, A.226, W.262, C.269 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.154, A:A.226, A:W.262 Hydrogen bonds: A:G.146, A:G.146, A:Q.147, A:A.226, A:R.228 LMT.10: 7 residues within 4Å: Chain A: S.238, L.241 Chain B: G.259, M.261, K.264, I.265, L.268 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:K.264, B:I.265, B:L.268 Hydrogen bonds: B:G.259 Salt bridges: B:K.264 LMT.11: 9 residues within 4Å: Chain B: F.144, G.146, Q.147, A.150, L.154, V.225, A.226, W.262, C.269 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.154, B:A.226, B:W.262 Hydrogen bonds: B:G.146, B:G.146, B:Q.147, B:A.226, B:R.228 LMT.13: 7 residues within 4Å: Chain B: S.238, L.241 Chain C: G.259, M.261, K.264, I.265, L.268 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:K.264, C:I.265, C:L.268 Hydrogen bonds: C:G.259 Salt bridges: C:K.264 LMT.14: 9 residues within 4Å: Chain C: F.144, G.146, Q.147, A.150, L.154, V.225, A.226, W.262, C.269 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.154, C:A.226, C:W.262 Hydrogen bonds: C:G.146, C:G.146, C:Q.147, C:A.226, C:R.228 LMT.16: 7 residues within 4Å: Chain C: S.238, L.241 Chain D: G.259, M.261, K.264, I.265, L.268 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:K.264, D:I.265, D:L.268 Hydrogen bonds: D:G.259 Salt bridges: D:K.264 LMT.17: 9 residues within 4Å: Chain D: F.144, G.146, Q.147, A.150, L.154, V.225, A.226, W.262, C.269 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:L.154, D:A.226, D:W.262 Hydrogen bonds: D:G.146, D:G.146, D:Q.147, D:A.226, D:R.228

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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