1I4M | pdb_00001i4m

Crystal structure of the human prion protein reveals a mechanism for oligomerization

• PDB DOI: https://doi.org/10.2210/pdb1I4M/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-02-22 Released: 2002-02-27 
• Deposition Author(s): Knaus, K.J., Morillas, M., Swietnicki, W., Malone, M., Surewicz, W.K., Yee, V.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal structure of the human prion protein reveals a mechanism for oligomerization.

Knaus, K.J., Morillas, M., Swietnicki, W., Malone, M., Surewicz, W.K., Yee, V.C.

(2001) Nat Struct Biol 8: 770-774

• PubMed: 11524679 
• DOI: https://doi.org/10.1038/nsb0901-770
• Primary Citation Related Structures: 
  1I4M


• PubMed Abstract: 
  

  The pathogenesis of transmissible encephalopathies is associated with the conversion of the cellular prion protein, PrP(C), into a conformationally altered oligomeric form, PrP(Sc). Here we report the crystal structure of the human prion protein in dimer form at 2 A resolution. The dimer results from the three-dimensional swapping of the C-terminal helix 3 and rearrangement of the disulfide bond. An interchain two-stranded antiparallel beta-sheet is formed at the dimer interface by residues that are located in helix 2 in the monomeric NMR structures. Familial prion disease mutations map to the regions directly involved in helix swapping. This crystal structure suggests that oligomerization through 3D domain-swapping may constitute an important step on the pathway of the PrP(C) --> PrP(Sc) conversion.

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Organizational Affiliation: 
• Department of Molecular Cardiology and Center for Structural Biology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue NB20, Cleveland, Ohio 44195, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 12.98 kDa 
• Atom Count: 1,005 
• Modeled Residue Count: 108 
• Deposited Residue Count: 108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAJOR PRION PROTEIN	A	108	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04156 (Homo sapiens) Explore P04156  Go to UniProtKB:  P04156
PHAROS:  P04156 GTEx:  ENSG00000171867

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.441	α = 90
b = 85.707	β = 90
c = 40.501	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-27 
Deposition Author(s): Knaus, K.J., Morillas, M., Swietnicki, W., Malone, M., Surewicz, W.K., Yee, V.C.

Revision History  

• Version 1.0: 2002-02-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary