6AXZ

Segment from bank vole prion protein 168-176 QYNNQNNFV


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 0.75 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Sub-angstrom cryo-EM structure of a prion protofibril reveals a polar clasp.

Gallagher-Jones, M.Glynn, C.Boyer, D.R.Martynowycz, M.W.Hernandez, E.Miao, J.Zee, C.T.Novikova, I.V.Goldschmidt, L.McFarlane, H.T.Helguera, G.F.Evans, J.E.Sawaya, M.R.Cascio, D.Eisenberg, D.S.Gonen, T.Rodriguez, J.A.

(2018) Nat Struct Mol Biol 25: 131-134

  • DOI: https://doi.org/10.1038/s41594-017-0018-0
  • Primary Citation of Related Structures:  
    6AXZ, 6BTK

  • PubMed Abstract: 

    The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named 'polar clasps'.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major prion protein9Myodes glareolusMutation(s): 0 
UniProt
Find proteins for Q8VHV5 (Myodes glareolus)
Explore Q8VHV5 
Go to UniProtKB:  Q8VHV5
Entity Groups  
UniProt GroupQ8VHV5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 0.75 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 4.94α = 94.21
b = 10.34β = 92.38
c = 31.15γ = 102.2
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references
  • Version 1.2: 2018-02-21
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references