3MD4 | pdb_00003md4

Prion peptide

• PDB DOI: https://doi.org/10.2210/pdb3MD4/pdb

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


• Deposited: 2010-03-29 Released: 2011-05-25 
• Deposition Author(s): Yee, V.C., Lee, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.169 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.148 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Literature

Diversity in the cross-beta spine structure of prion peptides

Lee, S., Yee, V.C.

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 1.25 kDa 
• Atom Count: 103 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major prion protein	A, B	6	N/A	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.169 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.148 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 9.439	α = 90
b = 17.792	β = 90
c = 44.561	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Yee, V.C., Lee, S.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references