SMTL ID : 8k8e.1

Human gamma-secretase in complex with a substrate mimetic

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

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: 7 residues within 4Å: Chain A: N.55, T.57, H.58, F.145, Y.173, W.648 Ligands: BMA-BMA-BMA.2 No protein-ligand interaction detected (PLIP)

1 x BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose

BMA-BMA-BMA.2: 2 residues within 4Å: Chain A: H.158 Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: P.43, L.44, N.45, E.188 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.44, A:E.188 Hydrogen bonds: A:P.43 NAG.4: 4 residues within 4Å: Chain A: V.383, L.431, A.433, N.435 No protein-ligand interaction detected (PLIP) NAG.5: 7 residues within 4Å: Chain A: W.533, I.537, N.573, G.576, T.577, V.578, V.621 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.578, A:V.621 Hydrogen bonds: A:S.536, A:S.536, A:N.573 NAG.6: 4 residues within 4Å: Chain A: N.530, Q.535, L.546, D.548 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.535 NAG.7: 3 residues within 4Å: Chain A: T.505, N.506, F.507 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.507 Hydrogen bonds: A:T.505 NAG.8: 3 residues within 4Å: Chain A: D.185, E.186, N.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.186

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

PC1.9: 7 residues within 4Å: Chain B: V.94, K.101, W.404 Chain C: F.6, V.131, A.139, L.142 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.6, C:V.131, B:V.94, B:K.101, B:W.404 Salt bridges: B:D.403

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.10: 4 residues within 4Å: Chain C: Y.69, L.199, L.203, L.206 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.69, C:L.199, C:L.203, C:L.206 CLR.11: 6 residues within 4Å: Chain C: R.186, W.188, L.192, S.223, W.227, I.230 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.188, C:L.192, C:W.227, C:I.230 CLR.12: 4 residues within 4Å: Chain C: Y.155, F.162, L.214, L.215 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.155, C:F.162, C:F.162, C:L.214, C:L.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Devkota, S. et al., Familial Alzheimer mutations stabilize synaptotoxic gamma-secretase-substrate complexes. Cell Rep (2024)

Release Date

2024-01-31

Peptides

Nicastrin: A
Presenilin-1: B
Gamma-secretase subunit APH-1A: C
Gamma-secretase subunit PEN-2: D
BOC-VAL-GLY-AIB-VAL-VAL-ILE-AIB-PHE-VAL-AIB-GLY-GLY-GLY-VAL-JUU-LEU-VLM: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
G

Membrane

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

Nicastrin

Presenilin-1

Gamma-secretase subunit APH-1A

Gamma-secretase subunit PEN-2

BOC-VAL-GLY-AIB-VAL-VAL-ILE-AIB-PHE-VAL-AIB-GLY-GLY-GLY-VAL-JUU-LEU-VLM

Related Entries With Identical Sequence