SMTL ID : 5a63.1

Cryo-EM structure of the human gamma-secretase complex at 3.4 angstrom resolution.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

hetero-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: 6 residues within 4Å: Chain A: I.42, P.43, L.44, N.45, E.188 Chain C: H.150 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 9 residues within 4Å: Chain A: S.151, Y.152, V.383, K.386, N.387, L.431, R.432, R.434, N.435 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.386 NAG-NAG.4: 8 residues within 4Å: Chain A: R.520, W.533, N.573, G.576, T.577, V.578, 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: 2 residues within 4Å: Chain A: Q.552, 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: 8 residues within 4Å: Chain A: N.55, A.56, T.57, H.58, F.145, Y.173, E.174, W.648 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: N.387, V.390 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.390 NAG.8: 3 residues within 4Å: Chain A: N.464, S.466, T.481 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain A: N.506 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.506 NAG.10: 5 residues within 4Å: Chain A: N.264, T.266, G.267, N.596, D.598 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.267, A:N.596, A:N.596 NAG.11: 2 residues within 4Å: Chain A: D.185, N.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.187

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

PC1.12: 14 residues within 4Å: Chain B: V.94, V.97, A.98, K.101, V.393, D.403, W.404, I.408, F.411 Chain C: F.6, V.131, I.135, A.139, L.142 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:V.131, C:I.135, B:V.94, B:V.97, B:K.101, B:V.393, B:W.404, B:I.408, B:F.411 Salt bridges: B:K.101 PC1.13: 16 residues within 4Å: Chain A: S.683, I.690, N.691, A.694, F.698 Chain C: P.16, L.20, T.24, R.31, R.115, Q.116, Y.119, L.169, F.173, V.176, G.225 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:P.16, C:L.20, C:T.24, C:Y.119, C:L.169, C:V.176, A:I.690, A:I.690 Hydrogen bonds: C:Q.116 Salt bridges: C:R.31, C:R.115, A:D.695

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bai, X. et al., An Atomic Structure of Human Gamma-Secretase. Nature (2015)

Release Date

2015-08-05

Peptides

Nicastrin: A
Presenilin-1: B
Gamma-secretase subunit APH-1A: 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

Gamma-secretase subunit APH-1A

Gamma-secretase subunit PEN-2

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