SMTL ID : 6idf.1

Cryo-EM structure of gamma secretase in complex with a Notch fragment

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 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: R.38, I.42, P.43, L.44, N.45, E.188 Chain C: H.150 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.150 NAG-NAG.3: 6 residues within 4Å: Chain A: Y.152, V.383, S.384, K.386, A.433, N.435 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: W.533, S.536, N.573, R.619, V.621 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.530, Q.535, D.548 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: S.544, Y.545, L.546, G.547, P.550, L.551, N.562 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-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-BMA-BMA.2: 6 residues within 4Å: Chain A: N.55, H.58, F.145, Y.173, E.174, W.648 No protein-ligand interaction detected (PLIP)

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

NAG.7: 1 residues within 4Å: Chain A: N.387 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.387 NAG.8: 2 residues within 4Å: Chain A: N.464, D.482 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.482 NAG.9: 3 residues within 4Å: Chain A: G.504, T.505, N.506 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.505, A:T.505, A:N.506 NAG.10: 6 residues within 4Å: Chain A: N.264, T.266, G.267, N.596, D.598, L.599 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.596, A:D.598 NAG.11: 2 residues within 4Å: Chain A: D.185, N.187 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain A: N.580 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.580

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

PC1.13: 12 residues within 4Å: Chain B: V.94, A.98, K.101, W.404, F.411 Chain C: F.6, L.35, A.39, I.127, I.135, A.139, L.142 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:A.98, B:W.404, B:F.411, B:F.411, B:F.411, C:F.6, C:L.35, C:A.39, C:I.135, C:A.139 PC1.14: 9 residues within 4Å: Chain B: R.128, E.243, W.244, L.248, A.251, L.443, V.444, F.447, Y.451 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.248, B:A.251, B:L.443, B:L.443, B:V.444, B:F.447, B:F.447, B:Y.451 Salt bridges: B:R.128, B:E.243 PC1.15: 19 residues within 4Å: Chain A: S.683, I.690, N.691, A.694, F.698 Chain C: P.16, L.20, T.24, S.113, R.115, Q.116, Y.119, L.169, V.176, G.225, L.226, A.228, F.229, A.232 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:I.690, A:F.698, C:P.16, C:L.20, C:T.24, C:Y.119, C:L.169, C:L.169, C:F.229 Hydrogen bonds: A:A.694, C:R.115 PC1.19: 9 residues within 4Å: Chain B: P.218, R.220 Chain D: N.2, L.3, F.28, L.31, F.35, W.36, E.40 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:P.218, D:F.28, D:L.31, D:F.35 Hydrogen bonds: D:L.3

3 x CLR: CHOLESTEROL(Covalent)(Non-covalent)

CLR.16: 7 residues within 4Å: Chain C: Y.69, I.73, L.199, G.202, L.203, F.205, L.206 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.73, C:F.205 CLR.17: 5 residues within 4Å: Chain C: W.188, L.192, S.223, W.227, I.230 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.188, C:W.188, C:W.227, C:W.227, C:W.227, C:I.230 CLR.18: 5 residues within 4Å: Chain C: Y.155, F.162, Y.210, L.214, L.215 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.155, C:F.162, C:Y.210, C:L.214, C:L.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, G. et al., Structural basis of Notch recognition by human gamma-secretase. Nature (2019)

Release Date

2018-12-26

Peptides

Nicastrin: A
Presenilin-1: B
Gamma-secretase subunit APH-1A: C
Gamma-secretase subunit PEN-2: D
Notch1: 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

Gamma-secretase subunit APH-1A

Gamma-secretase subunit PEN-2

Notch1

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