6BTK | pdb_00006btk

Segment from bank vole prion protein 168-176 QYNNQNNFV

• PDB DOI: https://doi.org/10.2210/pdb6BTK/pdb

• Classification: PROTEIN FIBRIL
• Organism(s): Myodes glareolus
• Mutation(s): No 


• Deposited: 2017-12-06 Released: 2018-01-17 
• Deposition Author(s): Glynn, C., Rodriguez, J.A., Boyer, D.R., Gallagher-Jones, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.162 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

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

• PubMed: 29335561 
• DOI: https://doi.org/10.1038/s41594-017-0018-0
• Primary Citation 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'.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA.
Department of Biological Chemistry and Department of Chemistry and Biochemistry, University of California Los Angeles, Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA.
Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA.
Laboratory of Pharmaceutical Biotechnology, Institute of Biology and Experimental Medicine, Buenos Aires, Argentina.
Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 1.14 kDa 
• Atom Count: 85 
• Modeled Residue Count: 9 
• Deposited Residue Count: 9 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major prion protein	A	9	Myodes glareolus	Mutation(s): 0
UniProt
Find proteins for Q8VHV5 (Myodes glareolus) Explore Q8VHV5  Go to UniProtKB:  Q8VHV5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.162 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 4.874	α = 93.36
b = 10.107	β = 91.15
c = 30.415	γ = 101.66

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Glynn, C., Rodriguez, J.A., Boyer, D.R., Gallagher-Jones, M.

Revision History  

• 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