4Y6K

Complex structure of presenilin homologue PSH bound to an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.85 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.320 
  • R-Value Observed: 0.322 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Cleavage of amyloid precursor protein by an archaeal presenilin homologue PSH

Dang, S.Wu, S.Wang, J.Li, H.Huang, M.He, W.Li, Y.M.Wong, C.C.Shi, Y.

(2015) Proc Natl Acad Sci U S A 112: 3344-3349

  • DOI: https://doi.org/10.1073/pnas.1502150112
  • Primary Citation of Related Structures:  
    4Y6K

  • PubMed Abstract: 

    Aberrant cleavage of amyloid precursor protein (APP) by γ-secretase contributes to the development of Alzheimer's disease. More than 200 disease-derived mutations have been identified in presenilin (the catalytic subunit of γ-secretase), making modulation of γ-secretase activity a potentially attractive therapeutic opportunity. Unfortunately, the technical challenges in dealing with intact γ-secretase have hindered discovery of modulators and demand a convenient substitute approach. Here we report that, similar to γ-secretase, the archaeal presenilin homolog PSH faithfully processes the substrate APP C99 into Aβ42, Aβ40, and Aβ38. The molar ratio of the cleavage products Aβ42 over Aβ40 by PSH is nearly identical to that by γ-secretase. The proteolytic activity of PSH is specifically suppressed by presenilin-specific inhibitors. Known modulators of γ-secretase also modulate PSH similarly in terms of the Aβ42/Aβ40 ratio. Structural analysis reveals association of a known γ-secretase inhibitor with PSH between its two catalytic aspartate residues. These findings identify PSH as a surrogate protease for the screening of agents that may regulate the protease activity and the cleavage preference of γ-secretase.


  • Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein PSH
A, B, C, D
301Methanoculleus marisnigri JR1Mutation(s): 5 
Gene Names: Memar_1924
Membrane Entity: Yes 
UniProt
Find proteins for A3CWV0 (Methanoculleus marisnigri (strain ATCC 35101 / DSM 1498 / JR1))
Explore A3CWV0 
Go to UniProtKB:  A3CWV0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3CWV0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4B5
Query on 4B5

Download Ideal Coordinates CCD File 
E [auth C],
F [auth D]
N-{(2R,4S,5S)-2-benzyl-5-[(tert-butoxycarbonyl)amino]-4-hydroxy-6-phenylhexanoyl}-L-leucyl-L-phenylalaninamide
C39 H52 N4 O6
MURCDOXDAHPNRQ-OWIQAHIBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.85 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.320 
  • R-Value Observed: 0.322 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.617α = 90
b = 201.691β = 90
c = 117.505γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Non-polymer description
  • Version 1.2: 2015-04-08
    Changes: Database references
  • Version 1.3: 2020-02-05
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2023-11-08
    Changes: Data collection, Database references, Refinement description