SMTL ID : 5o8f.1

Structure of a chimaeric beta3-alpha5 GABAA receptor in complex with nanobody Nb25 and pregnanolone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-5-2-3-mer

Ligands

5 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 13 residues within 4Å: Chain A: N.152, R.195, V.197, S.198, R.199, S.214, R.216 Chain F: N.30, Y.31, S.103, T.110, Y.112, D.113 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:D.113, A:R.195, A:R.199, A:S.212 NAG-NAG-BMA-MAN-MAN-MAN-MAN.2: 11 residues within 4Å: Chain B: N.152, R.195, V.197, S.198, R.199, S.214 Chain G: N.30, Y.31, S.103, Y.112, D.113 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain G Hydrogen bonds: B:R.195, B:R.199, G:D.113 NAG-NAG-BMA-MAN-MAN-MAN-MAN.3: 12 residues within 4Å: Chain C: N.152, R.195, V.197, S.198, R.199, S.214 Chain H: N.30, Y.31, S.103, T.110, Y.112, D.113 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain H Hydrogen bonds: C:R.195, C:R.199, C:S.212, H:D.113, H:D.113 NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 14 residues within 4Å: Chain D: N.152, R.195, V.197, S.198, R.199, S.212, S.214, R.216 Chain I: N.30, Y.31, S.103, T.110, Y.112, D.113 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain D Hydrogen bonds: I:D.113, D:R.195, D:R.199, D:S.212 NAG-NAG-BMA-MAN-MAN-MAN-MAN.5: 13 residues within 4Å: Chain E: N.152, R.195, V.197, S.198, R.199, S.214, R.216 Chain J: N.30, Y.31, S.103, T.110, Y.112, D.113 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain J Hydrogen bonds: E:R.195, E:R.199, E:S.212, J:D.113

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

NAG.6: 3 residues within 4Å: Chain A: P.81, N.83, H.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.83 NAG.7: 2 residues within 4Å: Chain B: N.83, H.122 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.83 NAG.9: 2 residues within 4Å: Chain C: N.83, H.122 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.83 NAG.11: 4 residues within 4Å: Chain D: P.81, L.82, N.83, H.122 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.83 NAG.15: 2 residues within 4Å: Chain E: N.83, H.122 No protein-ligand interaction detected (PLIP)

5 x P9N: Pregnanolone(Non-covalent)

P9N.8: 8 residues within 4Å: Chain B: I.300, A.303, T.304 Chain C: I.237, Q.240, V.241, W.244, P.328 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.237, C:V.241, C:W.244, C:W.244, C:W.244, B:I.300, B:A.303 P9N.10: 7 residues within 4Å: Chain C: A.303, T.304 Chain D: I.237, Q.240, V.241, W.244, P.328 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:A.303, D:I.237, D:V.241, D:W.244, D:W.244, D:W.244 P9N.12: 7 residues within 4Å: Chain D: A.303, T.304 Chain E: I.237, Q.240, V.241, W.244, P.328 7 PLIP interactions: 1 interactions with chain D, 6 interactions with chain E Hydrophobic interactions: D:A.303, E:I.237, E:V.241, E:W.244, E:W.244, E:W.244, E:W.244 P9N.13: 9 residues within 4Å: Chain A: I.237, Q.240, V.241, W.244, P.328 Chain E: I.300, A.303, T.304, Y.307 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:I.237, A:V.241, A:W.244, A:W.244, A:W.244, A:W.244, E:I.300, E:A.303 P9N.14: 8 residues within 4Å: Chain A: I.300, A.303, T.304 Chain B: I.237, Q.240, V.241, W.244, P.328 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.300, A:A.303, B:I.237, B:V.241, B:W.244, B:W.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, P.S. et al., Structural basis for GABAA receptor potentiation by neurosteroids. Nat. Struct. Mol. Biol. (2017)

Release Date

2017-11-01

Peptides

Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5: ABCDE
Nanobody Nb25: FJ
Nanobody Nb25: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
K

J
O

G
L

H
M

I
N

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 alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5

Nanobody Nb25

Nanobody Nb25

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