SMTL ID : 9fjf.1

Lysosomal transporting complex of beta-glucocerebrosidase (GCase) and lysosomal integral membrane protein 2 (LIMP-2) with bound Pro-macrobodies (Combined focus map)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

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.1: 4 residues within 4Å: Chain A: N.30, V.48, L.94, T.132 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.132

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

NAG-NAG.2: 2 residues within 4Å: Chain A: Y.79, N.168 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain A: K.206, C.207, M.209, N.211, Y.229, S.238, D.269 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.269 NAG-NAG.4: 3 residues within 4Å: Chain A: I.275, N.287, I.290 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: I.5, N.19, A.20, Y.22 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.5: 5 residues within 4Å: Chain A: D.324, R.344, Y.372, L.373, N.374 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: N.7, F.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.12 Hydrogen bonds: A:N.7 NAG.8: 4 residues within 4Å: Chain A: D.182, S.183, N.186, K.189 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.182 NAG.9: 2 residues within 4Å: Chain A: N.266, G.282 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain A: N.67 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain B: N.59 No protein-ligand interaction detected (PLIP) NAG.13: 3 residues within 4Å: Chain B: T.138, D.141, N.146 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.146 NAG.14: 1 residues within 4Å: Chain B: N.270 No protein-ligand interaction detected (PLIP)

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.11: 7 residues within 4Å: Chain A: D.216, V.230, I.241, T.327, V.329, A.341, K.343 No protein-ligand interaction detected (PLIP) MES.15: 6 residues within 4Å: Chain B: F.26, D.27, M.49 Chain D: N.32, I.52, F.54 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Water bridges: D:F.54 Hydrogen bonds: B:D.27 MES.16: 4 residues within 4Å: Chain B: C.4, G.46, R.48, E.50 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.48 MES.17: 5 residues within 4Å: Chain B: P.29, R.170, K.425, F.426, D.453 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dobert, J.P. et al., Cryo-TEM structure of beta-glucocerebrosidase in complex with its transporter LIMP-2. Nat Commun (2025)

Release Date

2025-04-09

Peptides

Lysosome membrane protein 2: A
Lysosomal acid glucosylceramidase: B
Nanobody Nb1: C
Nanobody Nb6: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Lysosome membrane protein 2

Lysosomal acid glucosylceramidase

Nanobody Nb1

Nanobody Nb6

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