› 8oqy

Electron Microscopy
3.3Å resolution

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

Released:
DOI: 10.2210/pdb8oqy/pdb
PDB entry 8oqy coloured by chain, front view.
PDB entry 8oqy coloured by chain, side view.
PDB entry 8oqy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Apo and Aβ46-bound γ-secretase structures provide insights into amyloid-β processing by the APH-1B isoform.
Odorčić I, Hamed MB, Lismont S, Chávez-Gutiérrez L, Efremov RG
OpenAccess logo Nat Commun 15 4479 (2024)
PMID: 38802343
Related structures: EMD-17112

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-273821 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (6 distinct):
Nicastrin Chain: A
Molecule details ›
Chain: A
Length: 717 amino acids
Theoretical weight: 79.37 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92542 (Residues: 1-709; Coverage: 100%)
Gene names: KIAA0253, NCSTN, UNQ1874/PRO4317
Sequence domains:
Presenilin-1 Chain: B
Molecule details ›
Chain: B
Length: 467 amino acids
Theoretical weight: 52.71 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P49768 (Residues: 1-467; Coverage: 100%)
Gene names: AD3, PS1, PSEN1, PSNL1
Sequence domains: Presenilin
Gamma-secretase subunit APH-1B Chain: C
Molecule details ›
Chain: C
Length: 257 amino acids
Theoretical weight: 28.48 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8WW43 (Residues: 1-257; Coverage: 100%)
Gene names: APH1B, PSFL, UNQ688/PRO1328
Sequence domains: Aph-1 protein
Gamma-secretase subunit PEN-2 Chain: D
Molecule details ›
Chain: D
Length: 101 amino acids
Theoretical weight: 12.04 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9NZ42 (Residues: 1-101; Coverage: 100%)
Gene names: MDS033, PEN2, PSENEN
Sequence domains: Presenilin enhancer-2 subunit of gamma secretase

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
2 bound ligands:
Ligand NAG 7 x NAG
Ligand PC1 3 x PC1
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-17112
Expression system: Trichoplusia ni

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