3O3U

Crystal Structure of Human Receptor for Advanced Glycation Endproducts (RAGE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.497 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 1.5 A crystal structure of human receptor for advanced glycation endproducts (RAGE) ectodomains reveals unique features determining ligand binding.

Park, H.Boyington, J.C.

(2010) J.Biol.Chem. 285: 40762-40770

  • DOI: 10.1074/jbc.M110.169276

  • PubMed Abstract: 
  • Interaction of the pattern recognition receptor, RAGE with key ligands such as advanced glycation end products (AGE), S100 proteins, amyloid β, and HMGB1 has been linked to diabetic complications, inflammatory and neurodegenerative disorders, and can ...

    Interaction of the pattern recognition receptor, RAGE with key ligands such as advanced glycation end products (AGE), S100 proteins, amyloid β, and HMGB1 has been linked to diabetic complications, inflammatory and neurodegenerative disorders, and cancer. To help answer the question of how a single receptor can recognize and respond to a diverse set of ligands we have investigated the structure and binding properties of the first two extracellular domains of human RAGE, which are implicated in various ligand binding and subsequent signaling events. The 1.5-Å crystal structure reveals an elongated molecule with a large basic patch and a large hydrophobic patch, both highly conserved. Isothermal titration calorimetry (ITC) and deletion experiments indicate S100B recognition by RAGE is an entropically driven process involving hydrophobic interaction that is dependent on Ca(2+) and on residues in the C'D loop (residues 54-67) of domain 1. In contrast, competition experiments using gel shift assays suggest that RAGE interaction with AGE is driven by the recognition of negative charges on AGE-proteins. We also demonstrate that RAGE can bind to dsDNA and dsRNA. These findings reveal versatile structural features of RAGE that help explain its ability to recognize of multiple ligands.


    Organizational Affiliation

    Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA. hajpark@scripps.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein, Advanced glycosylation end product-specific receptor
N
581Homo sapiensEscherichia coli (strain K12)
This entity is chimeric
Mutation(s): 0 
Gene Names: AGER (RAGE), malE
Find proteins for Q15109 (Homo sapiens)
Go to Gene View: AGER
Go to UniProtKB:  Q15109
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLR
Query on MLR

Download SDF File 
Download CCD File 
N
MALTOTRIOSE
AMYLOTRIOSE
C18 H32 O16
FYGDTMLNYKFZSV-PXXRMHSHSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
N
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.497 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.739α = 90.00
b = 89.308β = 90.00
c = 97.978γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
SERGUIdata collection
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-02
    Type: Advisory, Refinement description, Source and taxonomy