Refinement of RAGE-DNA complex in 3S58 without DNA

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 

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This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 3S58


The specificity of DNA recognition by the RAGE receptor.

Yatime, L.Andersen, G.R.

(2014) J Exp Med 211: 749-750

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Advanced glycosylation end product-specific receptor
A, B
223Homo sapiensMutation(s): 0 
Gene Names: AGERRAGE
UniProt & NIH Common Fund Data Resources
Find proteins for Q15109 (Homo sapiens)
Explore Q15109 
Go to UniProtKB:  Q15109
PHAROS:  Q15109
GTEx:  ENSG00000204305 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15109
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.221 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.92α = 90
b = 77.92β = 90
c = 224.387γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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