SMTL ID : 7xzh.1

Cryo-EM structure of human LRRC8A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.1: 16 residues within 4Å: Chain A: I.135, A.138, C.139, F.142, K.145, F.146, R.148, I.259, R.262, L.263, R.266, Q.267, I.270 Chain B: W.23, F.27, Y.30 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.138, A:A.138, A:F.142, A:F.142, A:F.142, A:F.142, A:F.142, A:F.142, A:K.145, A:L.263, A:Q.267, A:I.270, B:F.27, B:F.27, B:Y.30 Hydrogen bonds: A:R.266, A:R.266 Salt bridges: A:R.148, A:R.148, A:R.148, A:R.262, A:R.266 P5S.7: 17 residues within 4Å: Chain B: L.134, I.135, A.138, C.139, N.141, F.142, K.145, F.146, R.148, I.259, R.262, L.263, R.266, I.270 Chain C: W.23, F.27, Y.30 21 PLIP interactions: 16 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.134, B:I.135, B:A.138, B:N.141, B:F.142, B:F.142, B:F.142, B:F.142, B:F.142, B:K.145, B:I.270, C:W.23, C:F.27, C:F.27, C:Y.30, C:Y.30 Salt bridges: B:R.148, B:R.262, B:R.266, B:R.266, B:R.266 P5S.11: 16 residues within 4Å: Chain C: I.135, A.138, C.139, F.142, K.145, F.146, R.148, I.259, R.262, L.263, R.266, Q.267, I.270 Chain D: W.23, F.27, Y.30 23 PLIP interactions: 18 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:A.138, C:A.138, C:F.142, C:F.142, C:F.142, C:F.142, C:F.142, C:F.142, C:K.145, C:Q.267, C:I.270, D:F.27, D:F.27, D:Y.30, D:Y.30, D:Y.30 Hydrogen bonds: C:R.266, C:R.266 Salt bridges: C:R.148, C:R.148, C:R.148, C:R.262, C:R.266 P5S.13: 15 residues within 4Å: Chain D: I.135, A.138, C.139, F.142, K.145, F.146, R.148, R.262, L.263, R.266, Q.267, I.270 Chain E: W.23, F.27, Y.30 21 PLIP interactions: 16 interactions with chain D, 5 interactions with chain E Hydrophobic interactions: D:F.142, D:F.142, D:F.142, D:F.142, D:F.142, D:K.145, D:F.146, D:F.146, D:Q.267, D:I.270, E:W.23, E:F.27, E:Y.30, E:Y.30, E:Y.30 Hydrogen bonds: D:R.148 Salt bridges: D:R.148, D:R.262, D:R.266, D:R.266, D:R.266 P5S.17: 15 residues within 4Å: Chain E: I.135, A.138, C.139, F.142, K.145, F.146, R.148, R.262, L.263, R.266, Q.267, I.270 Chain F: W.23, F.27, Y.30 18 PLIP interactions: 15 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:I.135, E:A.138, E:A.138, E:F.142, E:F.142, E:F.142, E:F.142, E:K.145, E:Q.267, E:I.270, F:F.27, F:F.27, F:Y.30 Hydrogen bonds: E:R.262, E:R.266 Salt bridges: E:R.148, E:R.148, E:R.266 P5S.21: 16 residues within 4Å: Chain A: W.23, F.27, Y.30 Chain F: I.135, A.138, C.139, F.142, K.145, F.146, R.148, I.259, R.262, L.263, R.266, Q.267, I.270 22 PLIP interactions: 3 interactions with chain A, 19 interactions with chain F Hydrophobic interactions: A:F.27, A:Y.30, A:Y.30, F:I.135, F:A.138, F:A.138, F:F.142, F:F.142, F:F.142, F:F.142, F:F.142, F:F.142, F:K.145, F:Q.267, F:I.270 Hydrogen bonds: F:R.266, F:R.266 Salt bridges: F:R.148, F:R.148, F:R.262, F:R.266, F:R.266

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

POV.2: 11 residues within 4Å: Chain A: E.115, W.120, Y.124, L.128, Y.281, Y.285 Chain B: I.38, T.316, I.320, L.321 Ligands: CLR.5 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:W.120, A:W.120, A:Y.124, A:Y.124, A:L.128, B:I.38, B:T.316, B:I.320, B:L.321 Hydrogen bonds: A:Y.285 pi-Cation interactions: A:Y.281 POV.8: 12 residues within 4Å: Chain B: E.115, W.120, K.123, Y.124, L.128, L.130, Y.281, Y.285 Chain C: I.38, I.320, L.321 Ligands: CLR.9 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:W.120, B:W.120, B:Y.124, B:Y.124, B:L.128, B:L.130, C:I.38, C:I.320, C:L.321 Hydrogen bonds: B:Y.285 POV.12: 12 residues within 4Å: Chain C: E.115, W.120, K.123, Y.124, L.128, Y.281, Y.285 Chain D: I.38, T.316, I.320, L.321 Ligands: CLR.15 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:W.120, C:W.120, C:Y.124, C:Y.124, C:L.128, D:I.38, D:T.316, D:I.320, D:L.321 Hydrogen bonds: C:Y.285 pi-Cation interactions: C:Y.281 POV.14: 12 residues within 4Å: Chain D: E.115, W.120, K.123, Y.124, L.128, L.130, Y.281, Y.285 Chain E: I.38, I.320, L.321 Ligands: CLR.19 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:W.120, D:W.120, D:Y.124, D:Y.124, D:L.128, D:L.130, E:I.38, E:I.320, E:L.321 Hydrogen bonds: D:Y.285 pi-Cation interactions: D:Y.281 POV.18: 10 residues within 4Å: Chain E: E.115, W.120, Y.124, L.128, Y.285 Chain F: I.38, T.316, I.320, L.321 Ligands: CLR.23 11 PLIP interactions: 4 interactions with chain F, 7 interactions with chain E Hydrophobic interactions: F:I.38, F:T.316, F:I.320, F:L.321, E:W.120, E:W.120, E:Y.124, E:Y.124, E:L.128 Hydrogen bonds: E:Y.285 pi-Cation interactions: E:Y.281 POV.22: 13 residues within 4Å: Chain A: I.38, T.316, I.320, L.321 Chain F: E.115, W.120, K.123, Y.124, L.128, L.130, Y.281, Y.285 Ligands: CLR.3 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:W.120, F:W.120, F:Y.124, F:Y.124, F:L.128, F:L.130, A:I.38, A:T.316, A:L.321 Hydrogen bonds: F:Y.285

12 x CLR: CHOLESTEROL(Non-covalent)

CLR.3: 9 residues within 4Å: Chain A: T.316, K.319, I.320, S.323, F.324, S.327, F.331 Ligands: CLR.4, POV.22 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.316, A:F.324, A:F.331 CLR.4: 8 residues within 4Å: Chain A: V.286, K.319, S.323, I.326, S.327, I.330, F.331 Ligands: CLR.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.286, A:I.330, A:F.331 Hydrogen bonds: A:K.319, A:K.319 CLR.5: 6 residues within 4Å: Chain B: S.323, F.324, S.327, F.331 Ligands: POV.2, CLR.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.324, B:F.324, B:F.331 CLR.6: 7 residues within 4Å: Chain B: V.286, H.287, S.323, S.327, I.330, F.331 Ligands: CLR.5 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.286, B:H.287, B:I.330, B:I.330, B:F.331 CLR.9: 7 residues within 4Å: Chain C: I.320, S.323, F.324, S.327, F.331 Ligands: POV.8, CLR.10 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.320, C:F.324, C:F.324, C:F.331 CLR.10: 6 residues within 4Å: Chain C: V.286, S.323, S.327, I.330, F.331 Ligands: CLR.9 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.286, C:I.330, C:F.331 CLR.15: 6 residues within 4Å: Chain D: I.320, S.323, F.324, S.327 Ligands: POV.12, CLR.16 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.320, D:F.324, D:F.324 CLR.16: 8 residues within 4Å: Chain D: V.286, H.287, K.319, S.323, S.327, I.330, F.331 Ligands: CLR.15 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.286, D:I.330, D:F.331 CLR.19: 7 residues within 4Å: Chain E: I.320, S.323, F.324, S.327, F.331 Ligands: POV.14, CLR.20 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:I.320, E:F.324, E:F.331 CLR.20: 7 residues within 4Å: Chain E: V.286, K.319, S.323, S.327, I.330, F.331 Ligands: CLR.19 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:V.286, E:I.330, E:F.331 Hydrogen bonds: E:K.319 CLR.23: 5 residues within 4Å: Chain F: I.320, S.323, F.324, S.327 Ligands: POV.18 No protein-ligand interaction detected (PLIP) CLR.24: 7 residues within 4Å: Chain F: V.286, H.287, S.323, I.326, S.327, I.330, F.331 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:V.286, F:I.330, F:I.330, F:F.331

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., cryo-EM structure of human LRRC8A. To Be Published

Release Date

2023-06-07

Peptides

Volume-regulated anion channel subunit LRRC8A: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Volume-regulated anion channel subunit LRRC8A