4HMM

Crystal structure of mutant rabbit PRP 121-230 (S174N)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

N-Terminal Helix-Cap in alpha-Helix 2 Modulates beta-State Misfolding in Rabbit and Hamster Prion Proteins.

Sweeting, B.Brown, E.Khan, M.Q.Chakrabartty, A.Pai, E.F.

(2013) PLoS One 8: e63047-e63047

  • DOI: https://doi.org/10.1371/journal.pone.0063047
  • Primary Citation of Related Structures:  
    4HLS, 4HMM, 4HMR

  • PubMed Abstract: 

    Susceptibility of a particular species to prion disease is affected by small differences in the sequence of PrP and correlates with the propensity of its PrP to assume the β-state. A helix-cap motif in the β2-α2-loop of native α-helical rabbit PrP, a resistant species, contains sequence differences that influence intra- and interspecies transmission. To determine the effect the helix-cap motif on β-state refolding propensity, we mutated S170N, S174N, and S170N/S174N of the rabbit PrP helix-cap to resemble that of hamster PrP and conversely, N170S, N174S, and N170S/N174S of hamster PrP to resemble the helix-cap of rabbit PrP. High-resolution crystal structures (1.45-1.6 Å) revealed that these mutations ablate hydrogen-bonding interactions within the helix-cap motif in rabbit PrP(C). They also alter the β-state-misfolding propensity of PrP; the serine mutations in hamster PrP decrease the propensity up to 35%, whereas the asparagine mutations in rabbit PrP increase it up to 42%. Rapid dilution of rabbit and hamster into β-state buffer conditions causes quick conversion to β-state monomers. Kinetic monitoring using size-exclusion chromatography showed that the monomer population decreases exponentially mirrored by an increase in an octameric species. The monomer-octamer transition rates are faster for hamster than for rabbit PrP. The N170S/N174S mutant of hamster PrP has a smaller octamer component at the endpoint compared to the wild-type, whereas the kinetics of octamer formation in mutant and wild-type rabbit PrP are comparable. These findings demonstrate that the sequence of the β2-α2 helix-cap affects refolding to the β-state and subsequently, may influence susceptibility to prion disease.


  • Organizational Affiliation

    Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major prion protein
A, B
132Oryctolagus cuniculusMutation(s): 1 
Gene Names: PRNPPRP
UniProt
Find proteins for Q95211 (Oryctolagus cuniculus)
Explore Q95211 
Go to UniProtKB:  Q95211
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ95211
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.59α = 90
b = 86.25β = 90
c = 87.08γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description