4OF5

Refinement of RAGE-DNA complex in 3S59 without DNA

• PDB DOI: https://doi.org/10.2210/pdb4OF5/pdb

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


• Deposited: 2014-01-14 Released: 2014-04-23 
• Deposition Author(s): Yatime, L., Andersen, G.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3S59

Literature

The specificity of DNA recognition by the RAGE receptor.

Yatime, L., Andersen, G.R.

(2014) J Exp Med 211: 749-750

• PubMed: 24778420 
• DOI: https://doi.org/10.1084/jem.20132526
• Primary Citation of Related Structures:  
  4OF5, 4OFV


• PubMed Abstract: 
  

  A recent paper by Sirois et al. in The Journal of Experimental Medicine reports that the receptor for advanced glycation end-products (RAGE) promotes uptake of DNA into endosomes and lowers the immune recognition threshold for the activation of Toll-like receptor 9. Two crystal structures suggested that the DNA phosphate-deoxyribose backbone is recognized by RAGE through well-defined interactions. However, the electron densities for the DNA molecules are weak enough that the presented modeling of DNA is questionable, and models only containing RAGE account for the observed diffraction data just as well as the RAGE-DNA complexes presented by the authors.

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Organizational Affiliation: 

Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.39 kDa 
• Atom Count: 3,267 
• Modelled Residue Count: 425 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Advanced glycosylation end product-specific receptor	A, B	223	Homo sapiens	Mutation(s): 0  Gene Names: AGER, RAGE
UniProt & NIH Common Fund Data Resources
Find proteins for Q15109 (Homo sapiens) Explore Q15109  Go to UniProtKB:  Q15109
PHAROS:  Q15109 GTEx:  ENSG00000204305

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.235 
• R-Value Work: 0.220 
• R-Value Observed: 0.221 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.121	α = 90
b = 79.121	β = 90
c = 224.045	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-23 
Deposition Author(s): Yatime, L., Andersen, G.R.

Revision History  

• Version 1.0: 2014-04-23
  Type: Initial release
  
• Version 1.1: 2014-06-18
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary