SMTL ID : 9fax.1

CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-3-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 12 residues within 4Å: Chain D: N.141, R.184, V.186, S.187, R.188, S.203, R.205 Chain J: N.417, Y.418, Y.499, D.500, W.502 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain J Hydrogen bonds: D:R.188, J:D.500, J:D.500, D:R.184, D:R.184

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 4 residues within 4Å: Chain D: P.70, L.71, N.72, H.111 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 4 residues within 4Å: Chain E: P.70, L.71, N.72, H.111 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.3: 8 residues within 4Å: Chain E: N.141, E.182, R.184, V.186, S.187, R.188, S.203, R.205 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.188

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.5: 2 residues within 4Å: Chain F: N.72, H.111 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.6: 9 residues within 4Å: Chain F: N.141, E.182, R.184, S.187, R.188, N.189, S.203, F.204, R.205 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.189, F:R.184, F:R.188

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 4 residues within 4Å: Chain A: W.159, R.161, S.163, N.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.163, A:N.184 NAG.36: 3 residues within 4Å: Chain G: W.159, S.163, N.184 No protein-ligand interaction detected (PLIP)

5 x R16: HEXADECANE(Non-covalent)

R16.8: 6 residues within 4Å: Chain A: G.210, I.214, I.218 Chain E: F.285 Ligands: HEX.22, HEX.23 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:I.214, A:I.218, E:F.285 R16.9: 4 residues within 4Å: Chain A: W.232, R.383, I.384 Ligands: PLM.21 No protein-ligand interaction detected (PLIP) R16.12: 5 residues within 4Å: Chain A: I.281, F.282 Chain C: T.67, F.69 Ligands: CLR.11 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:F.69, A:I.281, A:I.281, A:F.282 R16.37: 5 residues within 4Å: Chain F: V.282 Chain G: G.210, I.214, I.218 Ligands: D10.30 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:V.282, G:I.214 R16.38: 6 residues within 4Å: Chain G: M.209, Y.217, F.390, C.391, N.394, W.398 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:Y.217, G:F.390, G:F.390, G:W.398

2 x PX2: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX2.10: 12 residues within 4Å: Chain A: M.209, Y.217, I.218, T.221, V.225, W.228, F.390, C.391, N.394, L.395, W.398, L.402 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.217, A:T.221, A:V.225, A:W.228, A:L.395, A:W.398, A:W.398 PX2.15: 10 residues within 4Å: Chain D: W.229, W.233, R.420, I.421, P.424, F.425 Chain G: T.292, Y.295, F.296 Ligands: PLM.40 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: D:W.229, D:W.233, D:I.421, D:P.424, D:F.425, D:F.425, G:F.296

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.11: 12 residues within 4Å: Chain A: L.274, A.389, F.393, V.396, S.400, Y.401 Chain C: F.47, S.65, F.66, T.67, L.92 Ligands: R16.12 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:L.274, A:L.274, A:F.393, A:V.396, A:Y.401, C:F.66, C:L.92 CLR.42: 11 residues within 4Å: Chain G: L.274, A.389, F.393, V.396, S.400, Y.401 Chain I: S.65, T.67, M.88, L.92 Ligands: PGW.43 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain I Hydrophobic interactions: G:L.274, G:L.274, G:A.389, G:F.393, G:F.393, G:V.396, G:Y.401, I:L.92

4 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

PGW.13: 14 residues within 4Å: Chain C: G.8, V.9, A.12, I.13, I.16, I.95, F.98, F.101, F.102, F.103, C.104, N.105, T.106, Y.110 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.12, C:I.13, C:I.16, C:I.95, C:F.98, C:F.102, C:T.106 Salt bridges: C:R.5 PGW.14: 16 residues within 4Å: Chain A: S.267, Y.268, I.281, F.284, S.285 Chain C: D.68, F.69, S.70, K.78 Chain F: N.209, I.210, G.211, I.214, L.215, M.219, I.222 13 PLIP interactions: 5 interactions with chain F, 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: F:I.214, F:I.214, F:L.215, F:I.222, C:F.69, A:I.281, A:F.284 Hydrogen bonds: F:G.211, C:D.68, C:F.69, C:S.70, A:S.267 Salt bridges: C:K.78 PGW.43: 16 residues within 4Å: Chain D: N.209, I.210, G.211, I.214 Chain G: S.267, Y.268, I.281, F.284 Chain I: T.67, D.68, F.69, S.70 Ligands: D10.20, PLM.40, HEX.41, CLR.42 7 PLIP interactions: 2 interactions with chain D, 2 interactions with chain I, 3 interactions with chain G Hydrophobic interactions: D:I.214, G:F.284 Hydrogen bonds: D:G.211, I:D.68, I:K.78, G:S.267, G:S.267 PGW.44: 13 residues within 4Å: Chain G: T.388, L.392 Chain I: A.12, I.13, I.16, I.95, F.98, S.99, F.101, F.102, F.103, C.104, Y.110 8 PLIP interactions: 7 interactions with chain I, 1 interactions with chain G Hydrophobic interactions: I:A.12, I:I.13, I:I.16, I:I.95, I:F.101, I:F.102, G:T.388 Hydrogen bonds: I:F.103

13 x HEX: HEXANE(Non-covalent)(Non-functional Binders)

HEX.16: 2 residues within 4Å: Chain D: G.279, F.283 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.283 HEX.17: 1 residues within 4Å: Chain D: W.418 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.418 HEX.19: 2 residues within 4Å: Chain D: L.286, F.293 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.286, D:F.293, D:F.293 HEX.22: 1 residues within 4Å: Ligands: R16.8 No protein-ligand interaction detected (PLIP) HEX.23: 5 residues within 4Å: Chain E: M.275, G.279, V.282, F.283 Ligands: R16.8 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.282, E:F.283 HEX.24: 4 residues within 4Å: Chain E: F.427, S.428, N.431, W.435 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.427 HEX.25: 2 residues within 4Å: Chain E: R.420, I.421 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.421 HEX.26: 1 residues within 4Å: Chain E: F.293 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.293 HEX.31: 4 residues within 4Å: Chain F: W.229, F.427, S.428, N.431 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:W.229, F:F.427 HEX.32: 2 residues within 4Å: Chain F: R.420, I.421 No protein-ligand interaction detected (PLIP) HEX.34: 2 residues within 4Å: Chain F: F.293 Ligands: PLM.28 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.293 HEX.35: 1 residues within 4Å: Chain F: W.435 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:W.435 HEX.41: 3 residues within 4Å: Chain G: S.285, E.289 Ligands: PGW.43 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:E.289

5 x D10: DECANE(Non-covalent)

D10.18: 3 residues within 4Å: Chain D: F.293, Y.296 Chain E: W.233 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:F.293, D:Y.296, D:Y.296, E:W.233, E:W.233, E:W.233 D10.20: 5 residues within 4Å: Chain D: I.214, M.219, W.435 Ligands: PLM.40, PGW.43 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.214, D:M.219, D:W.435 D10.27: 5 residues within 4Å: Chain A: Y.295, F.296 Chain F: I.226, V.230, W.233 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:Y.295, F:I.226, F:W.233, F:W.233 D10.29: 4 residues within 4Å: Chain F: L.429, F.430, Y.438 Ligands: D10.30 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.429, F:F.430, F:F.430, F:Y.438 D10.30: 7 residues within 4Å: Chain F: M.275, M.278, V.282, F.283, T.426 Ligands: D10.29, R16.37 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:V.282, F:F.283, F:F.283, F:T.426

5 x PLM: PALMITIC ACID(Non-covalent)

PLM.21: 9 residues within 4Å: Chain A: V.225, W.228, W.232 Chain E: L.289, F.293, Y.296, I.297, R.301 Ligands: R16.9 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:V.225, A:W.228, A:W.228, A:W.232, E:L.289, E:F.293, E:F.293, E:Y.296, E:I.297 Salt bridges: E:R.301 PLM.28: 3 residues within 4Å: Chain F: V.422, F.423 Ligands: HEX.34 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:V.422, F:F.423 PLM.33: 7 residues within 4Å: Chain F: L.289, F.293, Y.296, R.301 Chain G: V.225, W.232 Ligands: PLM.39 7 PLIP interactions: 4 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: F:L.289, F:F.293, F:Y.296, G:V.225, G:W.232, G:W.232 Salt bridges: F:R.301 PLM.39: 6 residues within 4Å: Chain G: W.228, W.232, R.383, I.384 Chain I: F.103 Ligands: PLM.33 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain I Hydrophobic interactions: G:W.228, G:R.383, G:I.384, I:F.103 PLM.40: 4 residues within 4Å: Chain G: V.288 Ligands: PX2.15, D10.20, PGW.43 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state. To Be Published

Release Date

2025-07-02

Peptides

Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2: AG
Neuroligin-2: BH
LHFPL tetraspan subfamily member 4 protein: CI
Gamma-aminobutyric acid receptor subunit beta-3: DEF
Megabody25: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

G
C

B
G

H
H

C
I

I
L

D
B

E
A

F
D

J
F

Membrane

We predict this structure to be a membrane protein.
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Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2

Neuroligin-2

LHFPL tetraspan subfamily member 4 protein

Gamma-aminobutyric acid receptor subunit beta-3

Megabody25

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