6AQ7

Structure of POM6 FAB fragment complexed with mouse PrPc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of POM6 Fab and mouse prion protein complex identifies key regions for prions conformational conversion.

Baral, P.K.Swayampakula, M.Aguzzi, A.James, M.N.G.

(2018) FEBS J. 285: 1701-1714

  • DOI: 10.1111/febs.14438

  • PubMed Abstract: 
  • Conversion of the cellular prion protein PrP <sup>C </sup> into its pathogenic isoform PrP <sup>S </sup> <sup>c </sup> is the hallmark of prion diseases, fatal neurodegenerative diseases affecting many mammalian species including humans. Anti-prion m ...

    Conversion of the cellular prion protein PrP C into its pathogenic isoform PrP S c is the hallmark of prion diseases, fatal neurodegenerative diseases affecting many mammalian species including humans. Anti-prion monoclonal antibodies can arrest the progression of prion diseases by stabilizing the cellular form of the prion protein. Here, we present the crystal structure of the POM6 Fab fragment, in complex with the mouse prion protein (moPrP). The prion epitope of POM6 is in close proximity to the epitope recognized by the purportedly toxic antibody fragment, POM1 Fab also complexed with moPrP. The POM6 Fab recognizes a larger binding interface indicating a likely stronger binding compared to POM1. POM6 and POM1 exhibit distinct biological responses. Structural comparisons of the bound mouse prion proteins from the POM6 Fab:moPrP and POM1 Fab:moPrP complexes reveal several key regions of the prion protein that might be involved in initiating mis-folding events.


    Organizational Affiliation

    Institute of Neuropathology, University of Zurich, Switzerland.,Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major prion protein
A
122Mus musculusMutation(s): 0 
Gene Names: Prnp (Prn-p, Prp)
Find proteins for P04925 (Mus musculus)
Go to UniProtKB:  P04925
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
POM6 FAB Heavy CHAIN
H
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
POM6 FAB light CHAIN
L
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, L
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
TCE
Query on TCE

Download SDF File 
Download CCD File 
H
3,3',3''-phosphanetriyltripropanoic acid
3-[bis(2-carboxyethyl)phosphanyl]propanoic acid
C9 H15 O6 P
PZBFGYYEXUXCOF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.197 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.040α = 90.00
b = 82.420β = 90.00
c = 103.700γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
MOLREPphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Alberta innovatesCanada--

Revision History 

  • Version 1.0: 2018-04-04
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references
  • Version 1.2: 2018-11-07
    Type: Data collection, Source and taxonomy