SMTL ID : 7mly.1

Cryo-EM reveals partially and fully assembled native glycine receptors,heteromeric pentamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.1: 3 residues within 4Å: Chain C: T.53 Chain I: N.66, E.197 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:E.197

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.2: 3 residues within 4Å: Chain J: N.66, S.68, Q.95 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: 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.3: 2 residues within 4Å: Chain K: N.66, E.200 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:E.200 NAG-NAG-BMA-MAN.4: 2 residues within 4Å: Chain L: N.66, E.197 No protein-ligand interaction detected (PLIP)

1 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.5: 4 residues within 4Å: Chain M: T.208, R.212, N.242, T.244 No protein-ligand interaction detected (PLIP)

9 x HP6: HEPTANE(Non-covalent)(Non-functional Binders)

HP6.6: 4 residues within 4Å: Chain I: I.264, R.427, P.431 Ligands: MYS.10 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:I.264 HP6.7: 5 residues within 4Å: Chain I: S.324, L.327, E.328, I.422 Ligands: DD9.8 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:I.422 HP6.18: 6 residues within 4Å: Chain J: S.324, E.328, A.331, I.422 Ligands: D12.17, LNK.20 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:I.422 HP6.19: 4 residues within 4Å: Chain J: W.271, R.427, P.431 Ligands: OCT.21 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:W.271, J:W.271 HP6.28: 4 residues within 4Å: Chain K: S.426, F.430, A.433 Ligands: DD9.29 No protein-ligand interaction detected (PLIP) HP6.36: 3 residues within 4Å: Chain K: W.271, R.427, I.428 No protein-ligand interaction detected (PLIP) HP6.48: 6 residues within 4Å: Chain M: V.331, I.334, A.335, L.338 Ligands: LNK.23, HP6.49 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:L.338 HP6.49: 5 residues within 4Å: Chain M: V.331, F.488, I.491, Y.496 Ligands: HP6.48 2 PLIP interactions: 2 interactions with chain M Hydrophobic interactions: M:V.331, M:F.488 HP6.50: 4 residues within 4Å: Chain M: W.289, R.478, A.479, P.482 No protein-ligand interaction detected (PLIP)

3 x DD9: nonane(Non-covalent)

DD9.8: 8 residues within 4Å: Chain I: F.321, S.324, I.422, I.425, F.430, A.433 Ligands: HP6.7, LNK.12 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:F.321, I:I.425 DD9.26: 5 residues within 4Å: Chain J: I.425, G.429, A.433, I.436 Ligands: D12.17 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:I.436 DD9.29: 7 residues within 4Å: Chain K: L.327, E.328, A.331, V.335, R.418, I.422 Ligands: HP6.28 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:I.422

10 x LNK: PENTANE(Non-functional Binders)(Non-covalent)

LNK.9: 4 residues within 4Å: Chain I: L.252, W.442 Ligands: MYS.10, NBU.14 No protein-ligand interaction detected (PLIP) LNK.12: 4 residues within 4Å: Chain I: G.429, M.432, A.433 Ligands: DD9.8 No protein-ligand interaction detected (PLIP) LNK.20: 5 residues within 4Å: Chain J: A.330, A.331, F.334 Chain K: W.271 Ligands: HP6.18 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain J Hydrophobic interactions: K:W.271, J:F.334 LNK.23: 4 residues within 4Å: Chain J: L.252, I.253 Chain M: V.326 Ligands: HP6.48 2 PLIP interactions: 1 interactions with chain M, 1 interactions with chain J Hydrophobic interactions: M:V.326, J:I.253 LNK.30: 6 residues within 4Å: Chain K: I.313, F.437, F.440, I.444, Y.445 Ligands: NBU.33 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:I.313, K:F.437, K:F.440, K:I.444 LNK.32: 5 residues within 4Å: Chain J: S.306 Chain K: G.249, L.252, I.253 Ligands: NBU.35 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:I.253 LNK.39: 3 residues within 4Å: Chain L: E.328, A.331 Ligands: D12.38 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:A.331 LNK.41: 3 residues within 4Å: Chain L: W.442 Ligands: OCT.40, NBU.45 No protein-ligand interaction detected (PLIP) LNK.51: 1 residues within 4Å: Ligands: LNK.53 No protein-ligand interaction detected (PLIP) LNK.53: 3 residues within 4Å: Chain M: M.270, L.497 Ligands: LNK.51 No protein-ligand interaction detected (PLIP)

1 x MYS: PENTADECANE(Non-covalent)

MYS.10: 8 residues within 4Å: Chain I: L.260, I.264, F.434, N.438, M.439, W.442 Ligands: HP6.6, LNK.9 No protein-ligand interaction detected (PLIP)

1 x D10: DECANE(Non-covalent)

D10.11: 7 residues within 4Å: Chain I: I.313, A.433, I.436, F.437, F.440, I.444, Y.445 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:I.313, I:F.437, I:F.437, I:F.440, I:F.440

9 x NBU: N-BUTANE(Non-covalent)(Non-functional Binders)

NBU.13: 4 residues within 4Å: Chain I: L.252, I.253 Ligands: NBU.14, NBU.43 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:I.253, I:I.253 NBU.14: 3 residues within 4Å: Chain I: L.252 Ligands: LNK.9, NBU.13 No protein-ligand interaction detected (PLIP) NBU.33: 3 residues within 4Å: Chain K: V.308, I.313 Ligands: LNK.30 No protein-ligand interaction detected (PLIP) NBU.34: 5 residues within 4Å: Chain K: L.252, W.442, K.446 Ligands: HEX.31, NBU.35 No protein-ligand interaction detected (PLIP) NBU.35: 3 residues within 4Å: Chain K: L.252 Ligands: LNK.32, NBU.34 No protein-ligand interaction detected (PLIP) NBU.42: 3 residues within 4Å: Chain L: I.313 Ligands: NBU.43, NBU.44 No protein-ligand interaction detected (PLIP) NBU.43: 3 residues within 4Å: Chain L: V.308 Ligands: NBU.13, NBU.42 No protein-ligand interaction detected (PLIP) NBU.44: 4 residues within 4Å: Chain L: F.437, F.440, I.444 Ligands: NBU.42 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:F.440, L:I.444 NBU.45: 2 residues within 4Å: Chain L: L.252 Ligands: LNK.41 No protein-ligand interaction detected (PLIP)

5 x GLY: GLYCINE(Non-covalent)

GLY.15: 8 residues within 4Å: Chain J: F.187, Y.230, T.232, F.235 Chain K: F.91, R.93, L.145, S.157 6 PLIP interactions: 2 interactions with chain K, 1 Ligand-Ligand interactions, 3 interactions with chain J Hydrogen bonds: K:S.157, G.15, J:F.187, J:F.187, J:T.232 Salt bridges: K:R.93 GLY.16: 7 residues within 4Å: Chain J: F.91, R.93, L.145, S.157 Chain M: F.204, Y.247, Y.253 5 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain M, 2 interactions with chain J Hydrogen bonds: G.16, M:F.204, M:Y.253, J:S.157 Salt bridges: J:R.93 GLY.27: 7 residues within 4Å: Chain K: F.187, Y.230, T.232, F.235 Chain L: R.93, L.145, S.157 5 PLIP interactions: 2 interactions with chain L, 3 interactions with chain K Hydrogen bonds: L:S.157, K:F.187, K:F.187, K:T.232 Salt bridges: L:R.93 GLY.37: 9 residues within 4Å: Chain I: F.91, R.93, L.145, S.157 Chain L: S.186, F.187, Y.230, T.232, F.235 5 PLIP interactions: 2 interactions with chain I, 1 Ligand-Ligand interactions, 2 interactions with chain L Hydrogen bonds: I:S.157, G.37, L:S.186, L:F.187 Salt bridges: I:R.93 GLY.47: 6 residues within 4Å: Chain I: F.187, T.232, F.235 Chain M: R.108, L.162, S.174 5 PLIP interactions: 2 Ligand-Ligand interactions, 1 interactions with chain I, 2 interactions with chain M Hydrogen bonds: G.47, G.47, I:F.187, M:S.174 Salt bridges: M:R.108

2 x D12: DODECANE(Non-covalent)

D12.17: 9 residues within 4Å: Chain J: F.321, S.324, I.422, I.425, S.426, F.430, A.433 Ligands: HP6.18, DD9.26 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:F.321, J:I.422, J:I.425 D12.38: 7 residues within 4Å: Chain L: F.321, K.421, I.422, I.425, F.430, A.433 Ligands: LNK.39 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:F.321, L:I.425, L:A.433

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

OCT.21: 5 residues within 4Å: Chain J: I.268, W.271 Chain M: V.345, V.349 Ligands: HP6.19 4 PLIP interactions: 1 interactions with chain M, 3 interactions with chain J Hydrophobic interactions: M:V.345, J:I.268, J:W.271, J:W.271 OCT.22: 4 residues within 4Å: Chain J: N.438, M.439, W.442, K.446 No protein-ligand interaction detected (PLIP) OCT.25: 6 residues within 4Å: Chain J: I.313, F.437, F.440, I.444, Y.445 Ligands: HEX.24 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:F.437, J:F.440, J:I.444 OCT.40: 5 residues within 4Å: Chain L: N.438, M.439, W.442, K.446 Ligands: LNK.41 No protein-ligand interaction detected (PLIP)

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

HEX.24: 3 residues within 4Å: Chain J: V.308, I.313 Ligands: OCT.25 No protein-ligand interaction detected (PLIP) HEX.31: 4 residues within 4Å: Chain K: N.438, M.439, W.442 Ligands: NBU.34 No protein-ligand interaction detected (PLIP) HEX.46: 4 residues within 4Å: Chain K: S.306 Chain L: G.249, L.252, I.253 No protein-ligand interaction detected (PLIP)

1 x UND: UNDECANE(Non-covalent)

UND.52: 8 residues within 4Å: Chain M: L.338, F.341, A.342, V.345, E.346, V.349, I.473, Y.476 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:Y.476

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, H. et al., Architecture and assembly mechanism of native glycine receptors. Nature (2021)

Release Date

2021-09-29

Peptides

3D1 Fab Light Chain: ACEG
3D1 Fab Heavy Chain: BDFH
Glycine receptor alpha 1: IJKL
Glycine receptor beta: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

C
K

E
M

G
I

B
G

D
F

F
L

H
H

I
D

J
A

K
B

L
C

M
E

Membrane

We predict this structure to be a membrane protein.
Show / Hide

3D1 Fab Light Chain

3D1 Fab Heavy Chain

Glycine receptor alpha 1

Glycine receptor beta

Related Entries With Identical Sequence