SMTL ID : 7a5v.1

CryoEM structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3 homopentamer, in complex with histamine and megabody Mb25 in lipid nanodisc

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 1.70 Å

Oligo State

hetero-5-5-mer

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: P.133, N.135, H.174 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: P.133, N.135, H.174 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain E: P.133, N.135, H.174 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain G: P.133, N.135, H.174 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 3 residues within 4Å: Chain I: P.133, N.135, H.174 No protein-ligand interaction detected (PLIP)

5 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.2: 13 residues within 4Å: Chain A: N.204, R.247, V.249, S.250, R.251, S.266, F.267, R.268 Chain B: N.417, Y.418, S.490, T.497, D.500 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.247, A:R.251, B:Y.418, B:Y.418, B:T.497 Water bridges: A:S.264, A:S.264, A:S.264 NAG-NAG-BMA-MAN-MAN.14: 13 residues within 4Å: Chain C: N.204, R.247, V.249, S.250, R.251, S.266, F.267, R.268 Chain D: N.417, Y.418, S.490, T.497, D.500 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:R.247, C:R.251, D:Y.418, D:Y.418, D:T.497 Water bridges: C:S.264, C:S.264, C:S.264 NAG-NAG-BMA-MAN-MAN.26: 13 residues within 4Å: Chain E: N.204, R.247, V.249, S.250, R.251, S.266, F.267, R.268 Chain F: N.417, Y.418, S.490, T.497, D.500 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.247, E:R.251, F:Y.418, F:Y.418, F:T.497 Water bridges: E:S.264, E:S.264, E:S.264 NAG-NAG-BMA-MAN-MAN.38: 13 residues within 4Å: Chain G: N.204, R.247, V.249, S.250, R.251, S.266, F.267, R.268 Chain H: N.417, Y.418, S.490, T.497, D.500 6 PLIP interactions: 1 interactions with chain H, 5 interactions with chain G Hydrogen bonds: H:Y.418, H:Y.418, G:R.247, G:R.251, H:T.497 Water bridges: G:S.264, G:S.264, G:S.264 NAG-NAG-BMA-MAN-MAN.50: 13 residues within 4Å: Chain I: N.204, R.247, V.249, S.250, R.251, S.266, F.267, R.268 Chain J: N.417, Y.418, S.490, T.497, D.500 6 PLIP interactions: 1 interactions with chain J, 5 interactions with chain I Hydrogen bonds: J:Y.418, J:Y.418, I:R.247, I:R.251, J:T.497 Water bridges: I:S.264, I:S.264, I:S.264

5 x R16: HEXADECANE(Non-covalent)

R16.3: 8 residues within 4Å: Chain A: W.292, P.380, F.383, S.384, N.387, W.391, V.395 Ligands: D10.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.292, A:F.383, A:W.391, A:V.395 R16.15: 8 residues within 4Å: Chain C: W.292, P.380, F.383, S.384, N.387, W.391, V.395 Ligands: D10.18 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.292, C:F.383, C:W.391, C:V.395 R16.27: 8 residues within 4Å: Chain E: W.292, P.380, F.383, S.384, N.387, W.391, V.395 Ligands: D10.30 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:W.292, E:F.383, E:W.391, E:V.395 R16.39: 8 residues within 4Å: Chain G: W.292, P.380, F.383, S.384, N.387, W.391, V.395 Ligands: D10.42 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:W.292, G:F.383, G:W.391, G:V.395 R16.51: 8 residues within 4Å: Chain I: W.292, P.380, F.383, S.384, N.387, W.391, V.395 Ligands: D10.54 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:W.292, I:F.383, I:W.391, I:V.395

20 x D10: DECANE(Non-covalent)

D10.4: 8 residues within 4Å: Chain A: I.289, V.293, W.296 Chain C: L.352, A.355, F.356, Y.359 Ligands: D10.5 Ligand excluded by PLIP D10.5: 4 residues within 4Å: Chain A: W.296, R.376, P.380 Ligands: D10.4 Ligand excluded by PLIP D10.6: 4 residues within 4Å: Chain A: S.384, W.391, L.392 Ligands: R16.3 Ligand excluded by PLIP D10.8: 4 residues within 4Å: Chain A: F.386, V.389, Y.393, Y.394 Ligand excluded by PLIP D10.16: 8 residues within 4Å: Chain C: I.289, V.293, W.296 Chain E: L.352, A.355, F.356, Y.359 Ligands: D10.17 Ligand excluded by PLIP D10.17: 4 residues within 4Å: Chain C: W.296, R.376, P.380 Ligands: D10.16 Ligand excluded by PLIP D10.18: 4 residues within 4Å: Chain C: S.384, W.391, L.392 Ligands: R16.15 Ligand excluded by PLIP D10.20: 4 residues within 4Å: Chain C: F.386, V.389, Y.393, Y.394 Ligand excluded by PLIP D10.28: 8 residues within 4Å: Chain E: I.289, V.293, W.296 Chain G: L.352, A.355, F.356, Y.359 Ligands: D10.29 Ligand excluded by PLIP D10.29: 4 residues within 4Å: Chain E: W.296, R.376, P.380 Ligands: D10.28 Ligand excluded by PLIP D10.30: 4 residues within 4Å: Chain E: S.384, W.391, L.392 Ligands: R16.27 Ligand excluded by PLIP D10.32: 4 residues within 4Å: Chain E: F.386, V.389, Y.393, Y.394 Ligand excluded by PLIP D10.40: 8 residues within 4Å: Chain G: I.289, V.293, W.296 Chain I: L.352, A.355, F.356, Y.359 Ligands: D10.41 Ligand excluded by PLIP D10.41: 4 residues within 4Å: Chain G: W.296, R.376, P.380 Ligands: D10.40 Ligand excluded by PLIP D10.42: 4 residues within 4Å: Chain G: S.384, W.391, L.392 Ligands: R16.39 Ligand excluded by PLIP D10.44: 4 residues within 4Å: Chain G: F.386, V.389, Y.393, Y.394 Ligand excluded by PLIP D10.52: 8 residues within 4Å: Chain A: L.352, A.355, F.356, Y.359 Chain I: I.289, V.293, W.296 Ligands: D10.53 Ligand excluded by PLIP D10.53: 4 residues within 4Å: Chain I: W.296, R.376, P.380 Ligands: D10.52 Ligand excluded by PLIP D10.54: 4 residues within 4Å: Chain I: S.384, W.391, L.392 Ligands: R16.51 Ligand excluded by PLIP D10.56: 4 residues within 4Å: Chain I: F.386, V.389, Y.393, Y.394 Ligand excluded by PLIP

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

NAG.7: 4 residues within 4Å: Chain A: N.63, S.65, F.66, E.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.63, A:E.69 NAG.19: 4 residues within 4Å: Chain C: N.63, S.65, F.66, E.69 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.63, C:E.69 NAG.31: 4 residues within 4Å: Chain E: N.63, S.65, F.66, E.69 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.63, E:E.69 NAG.43: 4 residues within 4Å: Chain G: N.63, S.65, F.66, E.69 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.63, G:E.69 NAG.55: 4 residues within 4Å: Chain I: N.63, S.65, F.66, E.69 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.63, I:E.69

5 x OCT: N-OCTANE(Non-covalent)

OCT.9: 6 residues within 4Å: Chain A: T.317, N.320, M.341, F.344 Chain I: P.283, L.286 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain I Hydrophobic interactions: A:N.320, A:M.341, A:F.344, A:F.344, I:P.283, I:L.286 OCT.21: 6 residues within 4Å: Chain A: P.283, L.286 Chain C: T.317, N.320, M.341, F.344 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:P.283, A:L.286, C:N.320, C:M.341, C:F.344, C:F.344 OCT.33: 6 residues within 4Å: Chain C: P.283, L.286 Chain E: T.317, N.320, M.341, F.344 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:N.320, E:M.341, E:F.344, E:F.344, C:P.283, C:L.286 OCT.45: 6 residues within 4Å: Chain E: P.283, L.286 Chain G: T.317, N.320, M.341, F.344 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain E Hydrophobic interactions: G:N.320, G:M.341, G:F.344, G:F.344, E:P.283, E:L.286 OCT.57: 6 residues within 4Å: Chain G: P.283, L.286 Chain I: T.317, N.320, M.341, F.344 6 PLIP interactions: 4 interactions with chain I, 2 interactions with chain G Hydrophobic interactions: I:N.320, I:M.341, I:F.344, I:F.344, G:P.283, G:L.286

5 x HSM: HISTAMINE(Non-covalent)

HSM.10: 8 residues within 4Å: Chain A: Y.152, E.210, S.211, Y.212, F.255, Y.260 Chain I: D.98, Y.117 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain A Hydrophobic interactions: I:Y.117 Hydrogen bonds: A:Y.152, A:Y.152 HSM.22: 8 residues within 4Å: Chain A: D.98, Y.117 Chain C: Y.152, E.210, S.211, Y.212, F.255, Y.260 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.117 Hydrogen bonds: C:Y.152, C:Y.152 HSM.34: 8 residues within 4Å: Chain C: D.98, Y.117 Chain E: Y.152, E.210, S.211, Y.212, F.255, Y.260 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:Y.117 Hydrogen bonds: E:Y.152, E:Y.152 HSM.46: 8 residues within 4Å: Chain E: D.98, Y.117 Chain G: Y.152, E.210, S.211, Y.212, F.255, Y.260 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain G Hydrophobic interactions: E:Y.117 Hydrogen bonds: G:Y.152, G:Y.152 HSM.58: 8 residues within 4Å: Chain G: D.98, Y.117 Chain I: Y.152, E.210, S.211, Y.212, F.255, Y.260 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain G Hydrogen bonds: I:Y.152, I:Y.152 Hydrophobic interactions: G:Y.117

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 4 residues within 4Å: Ligands: CL.23, CL.35, CL.47, CL.59 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: F.160, H.162, G.163 Chain C: K.158, S.159 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Ligands: CL.11, CL.35, CL.47, CL.59 Ligand excluded by PLIP CL.24: 5 residues within 4Å: Chain C: F.160, H.162, G.163 Chain E: K.158, S.159 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Ligands: CL.11, CL.23, CL.47, CL.59 Ligand excluded by PLIP CL.36: 5 residues within 4Å: Chain E: F.160, H.162, G.163 Chain G: K.158, S.159 Ligand excluded by PLIP CL.47: 4 residues within 4Å: Ligands: CL.11, CL.23, CL.35, CL.59 Ligand excluded by PLIP CL.48: 5 residues within 4Å: Chain G: F.160, H.162, G.163 Chain I: K.158, S.159 Ligand excluded by PLIP CL.59: 4 residues within 4Å: Ligands: CL.11, CL.23, CL.35, CL.47 Ligand excluded by PLIP CL.60: 5 residues within 4Å: Chain A: K.158, S.159 Chain I: F.160, H.162, G.163 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakane, T. et al., Single-particle cryo-EM at atomic resolution. Nature (2020)

Release Date

2020-11-18

Peptides

Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3: ACEGI
Megabody Mb25: BDFHJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

B
O

D
O

F
O

H
O

J
O

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3

Megabody Mb25

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