SMTL ID : 6qfa.1

CryoEM structure of a beta3K279T GABA(A)R homomer in complex with histamine and megabody Mb25

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-5-5-mer

Ligands

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.1: 12 residues within 4Å: Chain A: N.149, R.192, V.194, S.195, R.196, N.197, S.211, F.212, R.213 Chain B: N.417, Y.418, D.500 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.197, A:R.192, A:R.196, B:Y.418, B:Y.418 NAG-NAG-BMA-MAN-MAN.2: 12 residues within 4Å: Chain F: N.417, Y.418, D.500 Chain G: N.149, R.192, V.194, S.195, R.196, N.197, S.211, F.212, R.213 4 PLIP interactions: 2 interactions with chain G, 2 interactions with chain F Hydrogen bonds: G:N.197, F:Y.418, F:Y.418, G:R.192, G:R.196 NAG-NAG-BMA-MAN-MAN.3: 12 residues within 4Å: Chain E: N.417, Y.418, D.500 Chain H: N.149, R.192, V.194, S.195, R.196, N.197, S.211, F.212, R.213 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain E Hydrogen bonds: H:N.197, H:R.192, H:R.196, E:Y.418, E:Y.418 NAG-NAG-BMA-MAN-MAN.4: 12 residues within 4Å: Chain D: N.417, Y.418, D.500 Chain I: N.149, R.192, V.194, S.195, R.196, N.197, S.211, F.212, R.213 4 PLIP interactions: 2 interactions with chain I, 2 interactions with chain D Hydrogen bonds: I:N.197, I:R.192, I:R.196, D:Y.418, D:Y.418 NAG-NAG-BMA-MAN-MAN.5: 12 residues within 4Å: Chain C: N.417, Y.418, D.500 Chain J: N.149, R.192, V.194, S.195, R.196, N.197, S.211, F.212, R.213 4 PLIP interactions: 2 interactions with chain J, 2 interactions with chain C Hydrogen bonds: J:N.197, J:R.192, J:R.196, C:Y.418, C:Y.418

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

NAG.6: 3 residues within 4Å: Chain A: P.78, N.80, H.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.80 NAG.8: 3 residues within 4Å: Chain G: P.78, N.80, H.119 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.80 NAG.10: 3 residues within 4Å: Chain H: P.78, N.80, H.119 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.80 NAG.12: 3 residues within 4Å: Chain I: P.78, N.80, H.119 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.80 NAG.14: 3 residues within 4Å: Chain J: P.78, N.80, H.119 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.80

5 x HSM: HISTAMINE(Non-covalent)

HSM.7: 9 residues within 4Å: Chain A: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 Chain J: D.43, Y.62 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain J Hydrogen bonds: A:Y.97, A:Y.97, A:T.202, J:D.43 Hydrophobic interactions: J:Y.62 pi-Stacking: J:Y.62 HSM.9: 9 residues within 4Å: Chain A: D.43, Y.62 Chain G: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain A Hydrogen bonds: G:Y.97, G:Y.97, G:T.202, A:D.43 Hydrophobic interactions: A:Y.62 pi-Stacking: A:Y.62 HSM.11: 9 residues within 4Å: Chain G: D.43, Y.62 Chain H: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 6 PLIP interactions: 3 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:Y.97, H:Y.97, H:T.202, G:D.43 Hydrophobic interactions: G:Y.62 pi-Stacking: G:Y.62 HSM.13: 9 residues within 4Å: Chain H: D.43, Y.62 Chain I: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 6 PLIP interactions: 3 interactions with chain I, 3 interactions with chain H Hydrogen bonds: I:Y.97, I:Y.97, I:T.202, H:D.43 Hydrophobic interactions: H:Y.62 pi-Stacking: H:Y.62 HSM.15: 9 residues within 4Å: Chain I: D.43, Y.62 Chain J: Y.97, E.155, S.156, Y.157, F.200, T.202, Y.205 6 PLIP interactions: 3 interactions with chain J, 3 interactions with chain I Hydrogen bonds: J:Y.97, J:Y.97, J:T.202, I:D.43 Hydrophobic interactions: I:Y.62 pi-Stacking: I:Y.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uchanski, T. et al., Megabodies expand the nanobody toolkit for protein structure determination by single-particle cryo-EM. Nat.Methods (2021)

Release Date

2021-08-04

Peptides

Gamma-aminobutyric acid receptor subunit beta-3,Gamma-aminobutyric acid receptor subunit beta-3: AGHIJ
Outer membrane protein,Outer membrane protein,Outer membrane protein,Outer membrane protein,Uncharacterized protein,Uncharacterized protein,Mb-c7HopQ-Nb25: BCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

G
C

H
D

I
E

J
A

B
K

C
O

D
N

E
M

F
L

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

Outer membrane protein,Outer membrane protein,Outer membrane protein,Outer membrane protein,Uncharacterized protein,Uncharacterized protein,Mb-c7HopQ-Nb25

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