SMTL ID : 8oqy.1

Structure of apo form of human gamma-secretase PSEN1 APH-1B isoform reconstituted into lipid nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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: I.42, P.43, N.45, E.188 Chain C: H.149 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.42 NAG-NAG.3: 5 residues within 4Å: Chain A: N.530, Q.535, L.546, G.547, D.548 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: W.533, S.536, N.573, G.576, T.577, V.578, R.619, V.621 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-NAG.2: 7 residues within 4Å: Chain A: N.55, A.56, T.57, H.58, F.145, H.158, Y.173 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.158

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

NAG.5: 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.6: 5 residues within 4Å: Chain A: S.544, Y.545, L.546, L.551, N.562 No protein-ligand interaction detected (PLIP) NAG.7: 1 residues within 4Å: Chain A: N.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.187 NAG.8: 4 residues within 4Å: Chain A: N.264, N.596, D.598, L.599 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.598, A:L.599 Hydrogen bonds: A:D.598, A:D.598, A:D.598 NAG.9: 2 residues within 4Å: Chain A: N.464, D.482 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.482 NAG.10: 4 residues within 4Å: Chain A: N.580, L.581, T.582, Q.585 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.582 NAG.11: 2 residues within 4Å: Chain A: R.434, N.435 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.435

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

PC1.12: 10 residues within 4Å: Chain A: I.690, N.691, D.695, F.698, I.699 Chain C: T.24, R.31, R.114, L.115, Y.118 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:T.24, C:Y.118, C:Y.118, C:Y.118, C:Y.118, A:I.690, A:F.698 Salt bridges: C:R.31 PC1.13: 12 residues within 4Å: Chain B: V.94, V.97, A.98, K.101, S.102, G.402, W.404 Chain C: F.6, L.18, V.134, S.138, L.141 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:L.18, C:V.134, C:V.134, C:L.141, B:V.94, B:V.97, B:A.98, B:W.404, B:W.404 Salt bridges: B:K.101 PC1.14: 9 residues within 4Å: Chain C: S.152, Q.154, L.157, S.207, Y.208, Y.209, G.210, L.213, F.217 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.157, C:Y.209, C:L.213, C:L.213, C:F.217 Hydrogen bonds: C:Y.209, C:G.210 pi-Cation interactions: C:Y.209

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

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

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