SMTL ID : 6xev.1

CryoEM structure of GIRK2-PIP2/CHS - G protein-gated inwardly rectifying potassium channel GIRK2 with modulators cholesteryl hemisuccinate and PIP2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.1: 6 residues within 4Å: Chain A: K.41, W.42, R.43, K.145, K.150, K.151 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:K.41, A:K.41, A:W.42 Salt bridges: A:K.15, A:K.41, A:R.43, A:K.145, A:K.150, A:K.151, A:K.151 PIO.15: 6 residues within 4Å: Chain B: K.41, W.42, R.43, K.145, K.150, K.151 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:K.41, B:K.41, B:W.42 Salt bridges: B:K.15, B:K.41, B:R.43, B:K.145, B:K.150, B:K.151, B:K.151 PIO.19: 6 residues within 4Å: Chain C: K.41, W.42, R.43, K.145, K.150, K.151 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:K.41, C:K.41, C:W.42 Salt bridges: C:K.15, C:K.41, C:R.43, C:K.145, C:K.150, C:K.151, C:K.151 PIO.23: 6 residues within 4Å: Chain D: K.41, W.42, R.43, K.145, K.150, K.151 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:K.41, D:K.41, D:W.42 Salt bridges: D:K.15, D:K.41, D:R.43, D:K.145, D:K.150, D:K.151, D:K.151

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.2: 3 residues within 4Å: Chain A: R.43, L.47 Chain D: L.130 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.47, D:L.130 Salt bridges: A:R.43 Y01.16: 3 residues within 4Å: Chain A: L.130 Chain B: R.43, L.47 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.130, B:L.47 Salt bridges: B:R.43 Y01.20: 3 residues within 4Å: Chain B: L.130 Chain C: R.43, L.47 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.47, B:L.130 Salt bridges: C:R.43 Y01.24: 3 residues within 4Å: Chain C: L.130 Chain D: R.43, L.47 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.47, C:L.130 Salt bridges: D:R.43

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

K.3: 5 residues within 4Å: Chain A: T.105 Chain B: T.105 Chain C: T.105 Chain D: T.105 Ligands: K.22 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Metal complexes: B:T.105, C:T.105, C:T.105 K.4: 10 residues within 4Å: Chain A: I.106, G.107 Chain B: I.106, G.107 Chain C: I.106, G.107 Chain D: I.106, G.107 Ligands: K.5, K.22 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain B Metal complexes: A:I.106, C:I.106, D:I.106, B:I.106 K.5: 9 residues within 4Å: Chain A: G.107, Y.108 Chain B: G.107, Y.108 Chain C: G.107, Y.108 Chain D: G.107, Y.108 Ligands: K.4 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Metal complexes: D:G.107, D:Y.108, C:G.107, A:G.107, B:G.107 K.6: 1 residues within 4Å: Ligands: K.9 No protein-ligand interaction detected (PLIP) K.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.8: 1 residues within 4Å: Ligands: K.18 No protein-ligand interaction detected (PLIP) K.9: 3 residues within 4Å: Chain A: G.269 Chain D: G.269 Ligands: K.6 No protein-ligand interaction detected (PLIP) K.10: 4 residues within 4Å: Chain A: M.264 Chain B: M.264 Chain C: M.264 Chain D: M.264 No protein-ligand interaction detected (PLIP) K.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) K.18: 1 residues within 4Å: Ligands: K.8 No protein-ligand interaction detected (PLIP) K.22: 10 residues within 4Å: Chain A: T.105, I.106 Chain B: T.105, I.106 Chain C: T.105, I.106 Chain D: T.105, I.106 Ligands: K.3, K.4 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Metal complexes: B:T.105, D:T.105, A:T.105, C:T.105

4 x NA: SODIUM ION(Non-functional Binders)

NA.14: 3 residues within 4Å: Chain A: D.179, R.181, S.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.179 NA.17: 3 residues within 4Å: Chain B: D.179, R.181, S.183 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.183 NA.21: 3 residues within 4Å: Chain C: D.179, R.181, S.183 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.181 NA.25: 3 residues within 4Å: Chain D: D.179, R.181, S.183 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mathiharan, Y.K. et al., Structural insights into GIRK2 channel modulation by cholesterol and PIP2. Cell Rep (2021)

Release Date

2021-09-01

Peptides

G protein-activated inward rectifier potassium channel 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
I

D
M

Membrane

We predict this structure to be a membrane protein.
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G protein-activated inward rectifier potassium channel 2

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