6DU9 | pdb_00006du9

Crystal Structure of Human Prion Protein 90-231

• PDB DOI: https://doi.org/10.2210/pdb6DU9/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-06-20 Released: 2019-07-03 
• Deposition Author(s): Nonato, M.C., Rangel, V.L., Pavlovici, F.A.
• Funding Organization(s): Brazilian National Council for Scientific and Technological Development (CNPq), Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Prion Protein 90-231

Rangel, V.L., Nonato, M.C., Pavlovici, F.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.45 kDa 
• Atom Count: 747 
• Modeled Residue Count: 91 
• Deposited Residue Count: 141 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major prion protein	A	141	Homo sapiens	Mutation(s): 0  Gene Names: PRNP, ALTPRP, PRIP, PRP
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], D [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.17	α = 90
b = 72.17	β = 90
c = 158.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
XDS	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Nonato, M.C., Rangel, V.L., Pavlovici, F.A.

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Funding Organization	Location	Grant Number
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	141945/2018-4
Sao Paulo Research Foundation (FAPESP)	Brazil	2016/22929-0
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	2017/26559-5

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2021-11-17
  Changes: Database references, Derived calculations, Refinement description, Structure summary
• Version 1.3: 2023-10-11
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary