4DGI

Structure of POM1 FAB fragment complexed with human PrPc Fragment 120-230


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural studies on the folded domain of the human prion protein bound to the Fab fragment of the antibody POM1.

Baral, P.K.Wieland, B.Swayampakula, M.Polymenidou, M.Rahman, M.H.Kav, N.N.Aguzzi, A.James, M.N.

(2012) Acta Crystallogr D Biol Crystallogr 68: 1501-1512

  • DOI: 10.1107/S0907444912037328
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Prion diseases are neurodegenerative diseases characterized by the conversion of the cellular prion protein PrP(c) into a pathogenic isoform PrP(sc). Passive immunization with antiprion monoclonal antibodies can arrest the progression of prion diseas ...

    Prion diseases are neurodegenerative diseases characterized by the conversion of the cellular prion protein PrP(c) into a pathogenic isoform PrP(sc). Passive immunization with antiprion monoclonal antibodies can arrest the progression of prion diseases. Here, the crystal structure of the Fab fragment of an antiprion monoclonal antibody, POM1, in complex with human prion protein (huPrP(c)) has been determined to 2.4 Å resolution. The prion epitope of POM1 is in close proximity to the epitope recognized by the purportedly therapeutic antibody fragment ICSM18 Fab in complex with huPrP(c). POM1 Fab forms a 1:1 complex with huPrP(c) and the measured K(d) of 4.5 × 10(-7) M reveals moderately strong binding between them. Structural comparisons have been made among three prion-antibody complexes: POM1 Fab-huPrP(c), ICSM18 Fab-huPrP(c) and VRQ14 Fab-ovPrP(c). The prion epitopes recognized by ICSM18 Fab and VRQ14 Fab are adjacent to a prion glycosylation site, indicating possible steric hindrance and/or an altered binding mode to the glycosylated prion protein in vivo. However, both of the glycosylation sites on huPrP(c) are positioned away from the POM1 Fab binding epitope; thus, the binding mode observed in this crystal structure and the binding affinity measured for this antibody are most likely to be the same as those for the native prion protein in vivo.


    Related Citations: 
    • Crystallization and preliminary X-ray diffraction analysis of prion protein bound to the Fab fragment of the POM1 antibody.
      Baral, P.K., Wieland, B., Swayampakula, M., Polymenidou, M., Aguzzi, A., Kav, N.N., James, M.N.
      (2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1211

    Organizational Affiliation

    Department of Biochemistry, School of Translational Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton AB T6G 2H7, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major prion protein
A
111Homo sapiensMutation(s): 0 
Gene Names: PRNPPRIPPRPALTPRP
Find proteins for P04156 (Homo sapiens)
Go to UniProtKB:  P04156
NIH Common Fund Data Resources
PHAROS  P04156

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
POM1 Fab Heavy chain
H
218Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
POM1 Fab Light chain
L
213Mus musculusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download CCD File 
L
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.259 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.53α = 90
b = 105.92β = 95.08
c = 76.23γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references