4OI7

RAGE recognizes nucleic acids and promotes inflammatory responses to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.104 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA.

Sirois, C.M.Jin, T.Miller, A.L.Bertheloot, D.Nakamura, H.Horvath, G.L.Mian, A.Jiang, J.Schrum, J.Bossaller, L.Pelka, K.Garbi, N.Brewah, Y.Tian, J.Chang, C.Chowdhury, P.S.Sims, G.P.Kolbeck, R.Coyle, A.J.Humbles, A.A.Xiao, T.S.Latz, E.

(2013) J.Exp.Med. 210: 2447-2463

  • DOI: 10.1084/jem.20120201
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recognition of DNA and RNA molecules derived from pathogens or self-antigen is one way the mammalian immune system senses infection and tissue damage. Activation of immune signaling receptors by nucleic acids is controlled by limiting the access of D ...

    Recognition of DNA and RNA molecules derived from pathogens or self-antigen is one way the mammalian immune system senses infection and tissue damage. Activation of immune signaling receptors by nucleic acids is controlled by limiting the access of DNA and RNA to intracellular receptors, but the mechanisms by which endosome-resident receptors encounter nucleic acids from the extracellular space are largely undefined. In this study, we show that the receptor for advanced glycation end-products (RAGE) promoted DNA uptake into endosomes and lowered the immune recognition threshold for the activation of Toll-like receptor 9, the principal DNA-recognizing transmembrane signaling receptor. Structural analysis of RAGE-DNA complexes indicated that DNA interacted with dimers of the outermost RAGE extracellular domains, and could induce formation of higher-order receptor complexes. Furthermore, mice deficient in RAGE were unable to mount a typical inflammatory response to DNA in the lung, indicating that RAGE is important for the detection of nucleic acids in vivo.


    Organizational Affiliation

    Department of Medicine, Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA 01605.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Advanced glycosylation end product-specific receptor
A, B
223Homo sapiensMutation(s): 0 
Gene Names: AGER (RAGE)
Find proteins for Q15109 (Homo sapiens)
Go to Gene View: AGER
Go to UniProtKB:  Q15109
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*TP*GP*CP*AP*AP*CP*GP*AP*TP*GP*CP*TP*AP*CP*GP*AP*AP*CP*GP*TP*G)-3'E22N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*AP*CP*GP*TP*TP*CP*GP*TP*AP*GP*CP*AP*TP*CP*GP*TP*TP*GP*CP*AP*G)-3'F22N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.104 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.215 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 77.920α = 90.00
b = 77.920β = 90.00
c = 224.387γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
Blu-Icedata collection
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-30
    Type: Initial release