4P2Y

Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse S100A6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structure of the RAGE:S100A6 Complex Reveals a Unique Mode of Homodimerization for S100 Proteins.

Yatime, L.Betzer, C.Jensen, R.K.Mortensen, S.Jensen, P.H.Andersen, G.R.

(2016) Structure --: --

  • DOI: 10.1016/j.str.2016.09.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • S100 proteins are calcium-dependent regulators of homeostatic processes. Upon cellular response to stress, and notably during tumorigenesis, they relocalize to the extracellular environment where they induce pro-inflammatory signals by activating the ...

    S100 proteins are calcium-dependent regulators of homeostatic processes. Upon cellular response to stress, and notably during tumorigenesis, they relocalize to the extracellular environment where they induce pro-inflammatory signals by activating the receptor for advanced glycation end products (RAGE), thereby facilitating tumor growth and metastasis. Despite its importance in sustaining inflammation, the structural basis for RAGE-S100 crosstalk is still unknown. Here we report two crystal structures of the RAGE:S100A6 complex encompassing a full-length RAGE ectodomain. The structures, in combination with a comprehensive interaction analysis, suggest that the primary S100A6 binding site is formed by the RAGE C1 domain. Complex formation with S100A6 induces a unique dimeric conformation of RAGE that appears suited for signal transduction and intracellular effector recruitment. Intriguingly, S100A6 adopts a dimeric conformation radically different from all known S100 dimers. We discuss the physiological relevance of this non-canonical homodimeric form in vivo.


    Organizational Affiliation

    Department of Biomedicine, Danish Research Institute of Translational Neuroscience - DANDRITE, Aarhus University, Ole Worms Allé 1170, 8000 Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark. Electronic address: gra@mbg.au.dk.,Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus, Denmark. Electronic address: laure.yatime@inserm.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Advanced glycosylation end product-specific receptor
A
304Homo 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
MoleculeChainsSequence LengthOrganismDetails
Protein S100-A6
B
91Mus musculusMutation(s): 0 
Gene Names: S100a6 (Cacy)
Find proteins for P14069 (Mus musculus)
Go to UniProtKB:  P14069
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.187 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 76.780α = 90.00
b = 113.390β = 90.00
c = 140.320γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2016-11-23
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Refinement description