3HEQ

Human prion protein variant D178N with M129


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational diversity in prion protein variants influences intermolecular beta-sheet formation.

Lee, S.Antony, L.Hartmann, R.Knaus, K.J.Surewicz, K.Surewicz, W.K.Yee, V.C.

(2010) Embo J. 29: 251-262

  • DOI: 10.1038/emboj.2009.333
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A conformational transition of normal cellular prion protein (PrP(C)) to its pathogenic form (PrP(Sc)) is believed to be a central event in the transmission of the devastating neurological diseases known as spongiform encephalopathies. The common met ...

    A conformational transition of normal cellular prion protein (PrP(C)) to its pathogenic form (PrP(Sc)) is believed to be a central event in the transmission of the devastating neurological diseases known as spongiform encephalopathies. The common methionine/valine polymorphism at residue 129 in the PrP influences disease susceptibility and phenotype. We report here seven crystal structures of human PrP variants: three of wild-type (WT) PrP containing V129, and four of the familial variants D178N and F198S, containing either M129 or V129. Comparison of these structures with each other and with previously published WT PrP structures containing M129 revealed that only WT PrPs were found to crystallize as domain-swapped dimers or closed monomers; the four mutant PrPs crystallized as non-swapped dimers. Three of the four mutant PrPs aligned to form intermolecular beta-sheets. Several regions of structural variability were identified, and analysis of their conformations provides an explanation for the structural features, which can influence the formation and conformation of intermolecular beta-sheets involving the M/V129 polymorphic residue.


    Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major prion protein
A, B
142Homo sapiensMutation(s): 1 
Gene Names: PRNP (ALTPRP, PRIP, PRP)
Find proteins for P04156 (Homo sapiens)
Go to Gene View: PRNP
Go to UniProtKB:  P04156
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.206 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.489α = 90.00
b = 57.489β = 90.00
c = 168.013γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data collection
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description