4MA8

Crystal structure of mouse prion protein complexed with Chlorpromazine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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This is version 1.3 of the entry. See complete history


Literature

Structural basis of prion inhibition by phenothiazine compounds.

Baral, P.K.Swayampakula, M.Rout, M.K.Kav, N.N.Spyracopoulos, L.Aguzzi, A.James, M.N.

(2014) Structure 22: 291-303

  • DOI: https://doi.org/10.1016/j.str.2013.11.009
  • Primary Citation of Related Structures:  
    4MA7, 4MA8

  • PubMed Abstract: 

    Conformational transitions of the cellular form of the prion protein, PrP(C), into an infectious isoform, PrP(Sc), are considered to be central events in the progression of fatal neurodegenerative diseases known as transmissible spongiform encephalopathies. Tricyclic phenothiazine compounds exhibit antiprion activity; however, the underlying molecular mechanism of PrP(Sc) inhibition remains elusive. We report the molecular structures of two phenothiazine compounds, promazine and chlorpromazine bound to a binding pocket formed at the intersection of the structured and the unstructured domains of the mouse prion protein. Promazine binding induces structural rearrangement of the unstructured region proximal to β1, through the formation of a "hydrophobic anchor." We demonstrate that these molecules, promazine in particular, allosterically stabilize the misfolding initiator-motifs such as the C terminus of α2, the α2-α3 loop, as well as the polymorphic β2-α2 loop. Hence, the stabilization effects of the phenothiazine derivatives on initiator-motifs induce a PrP(C) isoform that potentially resists oligomerization.


  • Organizational Affiliation

    Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada. Electronic address: michael.james@ualberta.ca.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major prion proteinA [auth C]114Mus musculusMutation(s): 0 
Gene Names: PrnpPrn-pPrp
UniProt
Find proteins for P04925 (Mus musculus)
Explore P04925 
Go to UniProtKB:  P04925
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04925
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
POM1 heavy chainB [auth H]218Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
POM1 light chainC [auth L]213Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z80
Query on Z80

Download Ideal Coordinates CCD File 
D [auth C]3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine
C17 H19 Cl N2 S
ZPEIMTDSQAKGNT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Z80 BindingDB:  4MA8 EC50: min: 2000, max: 2000 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.262α = 90
b = 106.883β = 95.32
c = 75.594γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
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: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2022-10-12
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Refinement description