3NHD

GYVLGS segment 127-132 from human prion with V129


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystallographic studies of prion protein (PrP) segments suggest how structural changes encoded by polymorphism at residue 129 modulate susceptibility to human prion disease.

Apostol, M.I.Sawaya, M.R.Cascio, D.Eisenberg, D.

(2010) J Biol Chem 285: 29671-29675

  • DOI: 10.1074/jbc.C110.158303
  • Primary Citation of Related Structures:  
    3NHC, 3NHD

  • PubMed Abstract: 
  • A single nucleotide polymorphism (SNP) in codon 129 of the human prion gene, leading to a change from methionine to valine at residue 129 of prion protein (PrP), has been shown to be a determinant in the susceptibility to prion disease. However, the mole ...

    A single nucleotide polymorphism (SNP) in codon 129 of the human prion gene, leading to a change from methionine to valine at residue 129 of prion protein (PrP), has been shown to be a determinant in the susceptibility to prion disease. However, the molecular basis of this effect remains unexplained. In the current study, we determined crystal structures of prion segments having either Met or Val at residue 129. These 6-residue segments of PrP centered on residue 129 are "steric zippers," pairs of interacting β-sheets. Both structures of these "homozygous steric zippers" reveal direct intermolecular interactions between Met or Val in one sheet and the identical residue in the mating sheet. These two structures, plus a structure-based model of the heterozygous Met-Val steric zipper, suggest an explanation for the previously observed effects of this locus on prion disease susceptibility and progression.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-DOE Institute, UCLA, Los Angeles, California 90095-1570, USA.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major prion protein AB6Homo sapiensMutation(s): 1 
Gene Names: PRNPALTPRPPRIPPRP
Find proteins for P04156 (Homo sapiens)
Explore P04156 
Go to UniProtKB:  P04156
NIH Common Fund Data Resources
PHAROS:  P04156
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACY
Query on ACY

Download Ideal Coordinates CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.173α = 90
b = 18.959β = 90
c = 9.585γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance