SMTL ID : 7dfw.1

Cryo_EM structure of delta N-NPC1L1-CLR

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 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: 2 residues within 4Å: Chain A: N.497, L.500 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-NAG.2: 4 residues within 4Å: Chain A: N.909, S.912, V.1005, Q.1043 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.3: 3 residues within 4Å: Chain A: Q.399, H.400, N.1037 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: P.429, K.430, N.431 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.431 NAG.5: 1 residues within 4Å: Chain A: N.464 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.464 NAG.6: 1 residues within 4Å: Chain A: N.506 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.506 NAG.7: 5 residues within 4Å: Chain A: P.415, N.416, G.609, F.611, Q.612 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.415 Hydrogen bonds: A:N.416 NAG.8: 1 residues within 4Å: Chain A: N.479 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.479 NAG.9: 1 residues within 4Å: Chain A: N.927 No protein-ligand interaction detected (PLIP) NAG.10: 3 residues within 4Å: Chain A: E.1071, L.1072, N.1075 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.1071 Hydrogen bonds: A:E.1071, A:N.1075

1 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.11: 24 residues within 4Å: Chain A: Y.646, L.649, A.650, L.651, G.652, S.653, Y.654, L.719, Q.722, G.826, L.827, L.828, F.832, Q.833, Y.836, F.839, F.1213, A.1214, M.1218, L.1221, L.1251, L.1255, V.1256 Ligands: CLR.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.646, A:L.1221, A:L.1255, A:V.1256 Hydrogen bonds: A:Q.722, A:L.827, A:L.828

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.12: 25 residues within 4Å: Chain A: L.382, W.383, F.404, T.407, Q.409, M.616, E.618, L.621, I.625, L.696, V.697, A.768, Q.873, A.876, Y.886, F.887, L.890, F.894, A.898, P.899, Y.1062, I.1097, T.1098, F.1101, L.1234 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.382, A:W.383, A:W.383, A:F.1101, A:L.1234 Hydrogen bonds: A:Q.409, A:E.618, A:Q.873, A:Y.886, A:Y.1062

6 x CLR: CHOLESTEROL(Non-covalent)

CLR.13: 6 residues within 4Å: Chain A: F.1155, L.1158, W.1159, L.1245, L.1248, L.1249 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1155, A:L.1158, A:W.1159, A:L.1245, A:L.1248 CLR.14: 8 residues within 4Å: Chain A: L.370, E.374, Y.640, L.677, M.684, L.699, P.703, F.704 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.374, A:Y.640, A:L.677, A:L.699, A:P.703, A:F.704 CLR.15: 7 residues within 4Å: Chain A: W.344, W.347, L.358, P.362, V.363, L.785, L.786 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.344, A:W.347, A:L.358, A:L.358, A:P.362, A:V.363, A:L.786 CLR.16: 4 residues within 4Å: Chain A: F.759, A.762, L.763, R.770 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.759, A:L.763 CLR.17: 4 residues within 4Å: Chain A: L.649, Y.654, L.827 Ligands: P5S.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.654, A:Y.654, A:L.827 CLR.18: 8 residues within 4Å: Chain A: L.337, F.340, L.748, S.751, L.752, I.781, F.784, L.785 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.340, A:L.752, A:I.781

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, M. et al., Structural insights into the mechanism of human NPC1L1-mediated cholesterol uptake. Sci Adv (2021)

Release Date

2021-08-11

Peptides

NPC1-like intracellular cholesterol transporter 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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NPC1-like intracellular cholesterol transporter 1