SMTL ID : 8oqz.1

Structure of human gamma-secretase PSEN1 APH-1B isoform reconstituted into lipid nanodisc in complex with Ab46

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

3 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: 5 residues within 4Å: Chain A: R.38, I.42, P.43, N.45, E.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.38 NAG-NAG.2: 9 residues within 4Å: Chain A: W.533, S.536, I.537, N.573, G.576, T.577, V.578, R.619, V.621 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.619 NAG-NAG.3: 5 residues within 4Å: Chain A: N.55, A.56, T.57, H.58, Y.173 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: N.387, S.389 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.387, A:S.389 NAG.5: 3 residues within 4Å: Chain A: D.185, E.186, N.187 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.186 NAG.6: 4 residues within 4Å: Chain A: N.264, T.266, D.598, L.599 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.264, A:L.599 Hydrogen bonds: A:N.264, A:T.266, A:D.598 NAG.7: 7 residues within 4Å: Chain A: Y.152, K.386, N.387, L.431, R.432, A.433, N.435 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.387, A:N.435 NAG.8: 4 residues within 4Å: Chain A: N.530, Q.535, L.546, G.547 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.530, A:Q.535, A:L.546 NAG.9: 5 residues within 4Å: Chain A: S.544, Y.545, G.547, P.550, N.562 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.544, A:G.547, A:N.562 NAG.10: 2 residues within 4Å: Chain A: T.505, N.506 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.505 Hydrogen bonds: A:N.506 NAG.11: 1 residues within 4Å: Chain A: N.464 No protein-ligand interaction detected (PLIP)

14 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.12: 7 residues within 4Å: Chain A: L.673, F.677 Chain C: A.3, A.4, F.7, L.18 Ligands: PC1.15 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.673, A:F.677, C:A.3, C:F.7, C:F.7, C:L.18 Salt bridges: A:K.666 PC1.13: 9 residues within 4Å: Chain B: W.244, S.254, V.255, I.437, T.440, L.443, F.447, A.448, Y.451 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.255, B:I.437, B:T.440, B:L.443, B:F.447, B:F.447 Hydrogen bonds: B:Y.451 PC1.14: 2 residues within 4Å: Chain B: L.420, F.428 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.420 PC1.15: 6 residues within 4Å: Chain B: V.94, S.102, Y.189 Ligands: PC1.12, PC1.16, PC1.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.94 PC1.16: 13 residues within 4Å: Chain B: V.94, V.97, K.101, S.102, W.404, I.408 Chain C: F.6, L.35, M.127, V.130, S.138, L.141 Ligands: PC1.15 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:V.94, B:K.101, B:W.404, B:W.404, B:I.408, C:F.6, C:L.35, C:V.130 Salt bridges: B:K.101 PC1.17: 8 residues within 4Å: Chain B: V.87, L.91, R.220, Q.223, A.224, M.228 Ligands: PC1.18, PC1.22 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.87, B:L.91, B:A.224 PC1.18: 7 residues within 4Å: Chain B: L.221, Y.225, M.228 Chain D: F.28 Ligands: PC1.17, PC1.19, PC1.25 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.221, B:Y.225 PC1.19: 6 residues within 4Å: Chain B: V.95, Y.181, L.201, M.228 Chain D: F.28 Ligands: PC1.18 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:V.95, B:Y.181, B:L.201, B:L.201, D:F.28, D:F.28 PC1.20: 5 residues within 4Å: Chain A: F.682 Chain C: V.221, G.224, T.225 Ligands: PC1.21 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.221, C:T.225, A:F.682 PC1.21: 16 residues within 4Å: Chain A: V.686, I.690, N.691, F.698 Chain C: P.16, T.24, R.31, S.112, R.114, L.115, Y.118, L.168, I.175, F.228, A.231 Ligands: PC1.20 16 PLIP interactions: 5 interactions with chain A, 11 interactions with chain C Hydrophobic interactions: A:V.686, A:I.690, A:F.698, A:F.698, A:F.698, C:P.16, C:Y.118, C:Y.118, C:L.168, C:I.175, C:F.228, C:F.228, C:A.231 Hydrogen bonds: C:R.31, C:S.112 Salt bridges: C:R.114 PC1.22: 5 residues within 4Å: Chain B: L.91, F.411 Chain C: Y.21 Ligands: PC1.15, PC1.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.411 PC1.23: 9 residues within 4Å: Chain C: S.152, Q.154, L.157, F.161, S.207, Y.208, Y.209, G.210, L.213 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Q.154, C:L.157, C:F.161, C:F.161 Hydrogen bonds: C:S.152, C:Y.209 pi-Cation interactions: C:Y.209 PC1.24: 6 residues within 4Å: Chain B: F.186, V.191 Chain D: T.72, I.75, Q.79, I.80 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.186, B:V.191 PC1.25: 8 residues within 4Å: Chain B: P.218, L.221 Chain D: F.28, F.35, W.36, F.38, R.39 Ligands: PC1.18 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:F.28, D:F.35, D:F.35, D:F.35, D:F.35, D:F.38, D:F.38, B:P.218, B:L.221 Salt bridges: D:R.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Odorcic, I. et al., Apo and A beta 46-bound gamma-secretase structures provide insights into amyloid-beta processing by the APH-1B isoform. Nat Commun (2024)

Release Date

2024-04-24

Peptides

Nicastrin: A
Presenilin-1 CTF12: B
Gamma-secretase subunit APH-1B: C
Gamma-secretase subunit PEN-2: D
Amyloid-beta peptide 1-46: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Nicastrin

Presenilin-1 CTF12

Gamma-secretase subunit APH-1B

Gamma-secretase subunit PEN-2

Amyloid-beta peptide 1-46

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