4XYN

X-ray structure of Ca(2+)-S100B with human RAGE-derived W61 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insights into the binding of the human receptor for advanced glycation end products (RAGE) by S100B, as revealed by an S100B-RAGE-derived peptide complex.

Jensen, J.L.Indurthi, V.S.Neau, D.B.Vetter, S.W.Colbert, C.L.

(2015) Acta Crystallogr.,Sect.D 71: 1176-1183

  • DOI: 10.1107/S1399004715004216

  • PubMed Abstract: 
  • S100B is a damage-associated molecular pattern protein that, when released into the extracellular milieu, triggers initiation of the inflammatory response through the receptor for advanced glycation end products (RAGE). Recognition of S100B is accomp ...

    S100B is a damage-associated molecular pattern protein that, when released into the extracellular milieu, triggers initiation of the inflammatory response through the receptor for advanced glycation end products (RAGE). Recognition of S100B is accomplished via the amino-terminal variable immunoglobulin domain (V-domain) of RAGE. To gain insights into this interaction, a complex between S100B and a 15-amino-acid peptide derived from residues 54-68 of the V-domain was crystallized. The X-ray crystal structure was solved to 2.55 Å resolution. There are two dimers of S100B and one peptide in the asymmetric unit. The binding interface of this peptide is compared with that found in the complex between S100B and the 12-amino-acid CapZ-derived peptide TRTK-12. This comparison reveals that although the peptides adopt completely different backbone structures, the residues buried at the interface interact with S100B in similar regions to form stable complexes. The binding affinities of S100B for the intact wild-type V-domain and a W61A V-domain mutant were determined to be 2.7 ± 0.5 and 1.3 ± 0.7 µM, respectively, using fluorescence titration experiments. These observations lead to a model whereby conformational flexibility in the RAGE receptor allows the adoption of a binding conformation for interaction with the stable hydrophobic groove on the surface of S100B.


    Organizational Affiliation

    NE-CAT, Bldg. 436E, Department of Chemistry and Chemical Biology, Cornell University, 9700 South Cass Avenue,, Argonne, IL 60439, USA.,Department of Chemistry and Biochemistry, North Dakota State University, PO Box 6050, Fargo, ND 58108-6050, USA.,Department of Pharmaceutical Sciences, North Dakota State University, PO Box 6050, Fargo, ND 58108-6050, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Receptor for advanced glycation endproducts-derived peptide (W61)
P
15Homo 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-B
A, B, C, D
92Homo sapiensMutation(s): 0 
Gene Names: S100B
Find proteins for P04271 (Homo sapiens)
Go to Gene View: S100B
Go to UniProtKB:  P04271
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.785α = 90.00
b = 86.684β = 90.00
c = 66.534γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
ADSCdata collection
XDSdata scaling
AutoPROCdata scaling
PHENIXrefinement
BALBESphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release
  • Version 1.1: 2015-05-20
    Type: Database references
  • Version 1.2: 2015-05-27
    Type: Data collection
  • Version 1.3: 2017-11-22
    Type: Advisory, Derived calculations, Refinement description, Source and taxonomy