4MA7

Crystal structure of mouse prion protein complexed with Promazine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

Starting Model: experimental
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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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major prion protein114Mus 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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P2Z
Query on P2Z

Download Ideal Coordinates CCD File 
D [auth A]Promazine
C17 H20 N2 S
ZGUGWUXLJSTTMA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
P2Z BindingDB:  4MA7 EC50: 5000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.211α = 90
b = 106.038β = 95.68
c = 75.733γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
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: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-27
    Changes: Structure summary