Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 0.79 kDa 
• Atom Count: 56 
• Residue Count: 6 
• Unique protein chains: 1

3NVF

IIHFGS segment 138-143 from human prion

• DOI: 10.2210/pdb3NVF/pdb

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2010-07-08 Released: 2011-03-02 
• Deposition Author(s): Apostol, M.I., Sawaya, M.R., Eisenberg, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 

Literature

Atomic structures suggest determinants of transmission barriers in Mammalian prion disease.

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

(2011) Biochemistry 50: 2456-2463

• PubMed: 21323366 
• DOI: 10.1021/bi101803k
• Primary Citation of Related Structures:  
  3NVE, 3NVF, 3NVG, 3NVH


• PubMed Abstract: 
  

Prion represents a unique class of pathogens devoid of nucleic acid. The deadly diseases transmitted by it between members of one species and, in certain instances, to members of other species present a public health concern. Transmissibility and the barriers to transmission between species have been suggested to arise from the degree to which a pathological protein conformation from an individual of one species can seed a pathological conformation in another species. However, this hypothesis has never been illustrated at an atomic level. Here we present three X-ray atomic structures of the same segment from human, mouse, and hamster PrP, which is critical for forming amyloid and confers species specificity in PrP seeding experiments. The structures reveal that different sequences encode different steric zippers and suggest that the degree of dissimilarity of these zipper structures gives rise to transmission barriers in prion disease, such as those that protect humans from acquiring bovine spongiform encephalopathy (BSE) and chronic wasting disease (CWD).

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Organizational Affiliation: 

Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, UCLA-DOE Institute, UCLA, 611 Charles Young Drive East, Los Angeles, California 90095-1570, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major prion protein	A	6	Homo sapiens	Mutation(s): 0  Gene Names: PRNP, ALTPRP, PRIP, PRP
Find proteins for P04156 (Homo sapiens) Explore P04156  Go to UniProtKB:  P04156
NIH Common Fund Data Resources
PHAROS:  P04156 GTEx:  ENSG00000171867

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.226 
• R-Value Work: 0.212 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.546	α = 90
b = 31.017	β = 90
c = 4.804	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-08 
• Released Date: 2011-03-02 
Deposition Author(s): Apostol, M.I., Sawaya, M.R., Eisenberg, D.

Revision History 

• Version 1.0: 2011-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance