4OI7 | pdb_00004oi7

RAGE recognizes nucleic acids and promotes inflammatory responses to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.237 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4OI7

This is version 1.2 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 Medicine 210: 2447-2463

  • DOI: https://doi.org/10.1084/jem.20120201
  • Primary Citation Related Structures: 
    4OI7, 4OI8

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 62.14 kDa 
  • Atom Count: 4,228 
  • Modeled Residue Count: 470 
  • Deposited Residue Count: 490 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  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
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Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
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'C [auth E]22N/A
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
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'D [auth F]22N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.237 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
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
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary