1W0W

Crystal Structure Of HLA-B*2709 Complexed With the self-Peptide TIS from EGF-response factor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Thermodynamic and Structural Equivalence of Two Hla-B27 Subtypes Complexed with a Self-Peptide

Hulsmeyer, M.Welfle, K.Pohlmann, T.Misselwitz, R.Alexiev, U.Welfle, H.Saenger, W.Uchanska-Ziegler, B.Ziegler, A.

(2005) J.Mol.Biol. 346: 1367

  • DOI: 10.1016/j.jmb.2004.12.047
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The F pocket of major histocompatibility complex (in humans HLA) class I molecules accommodates the C terminus of the bound peptide. Residues forming this pocket exhibit considerable polymorphism, and a single difference (Asp116 in HLA-B*2705 and His ...

    The F pocket of major histocompatibility complex (in humans HLA) class I molecules accommodates the C terminus of the bound peptide. Residues forming this pocket exhibit considerable polymorphism, and a single difference (Asp116 in HLA-B*2705 and His116 in HLA-B*2709 heavy chains) confers differential association of these two HLA-B27 subtypes to the autoimmune disease ankylosing spondylitis. As peptide presentation by HLA molecules is of central importance for immune responses, we performed thermodynamic (circular dichroism, differential scanning calorimetry, fluorescence polarization) and X-ray crystallographic analyses of both HLA-B27 subtypes complexed with the epidermal growth factor response factor 1-derived self-peptide TIS (RRLPIFSRL) to understand the impact of the Asp116His exchange on peptide display. This peptide is known to be presented in vivo by both subtypes, and as expected for a self-peptide, TIS-reactive cytotoxic T lymphocytes are absent in the respective individuals. The thermodynamic analyses reveal that both HLA-B27:TIS complexes exhibit comparable, relatively high thermostability (Tm approximately 60 degrees C) and undergo multi-step unfolding reactions, with dissociation of the peptide in the first step. As shown by X-ray crystallography, only subtle structural differences between the subtypes were observed regarding the architecture of their F pockets, including the presence of distinct networks of water molecules. However, no consistent structural differences were found between the peptide presentation modes. In contrast to other peptides displayed by the two HLA-subtypes which show either structural or dynamical differences in their peptide presentation modes, the TIS-complexed HLA-B*2705 and HLA-B*2709 subtypes are an example for thermodynamic and structural equivalence, in agreement with functional data.


    Related Citations: 
    • Dual, Hla-B27 Subtype-Dependent Conformation of a Self-Peptide
      Hulsmeyer, M.,Fiorillo, M.T.,Bettosini, F.,Sorrentino, R.,Saenger, W.,Ziegler, A.,Uchanska-Ziegler, B.
      (2004) J.Exp.Med. 199: 271
    • Thermodynamic and Structural Analysis of Peptide- and Allele-Dependent Properties of Two Hla-B27 Subtypes Exhibiting Differential Disease Association
      Hillig, R.C.,Hulsmeyer, M.,Saenger, W.,Welfle, K.,Misselwitz, R.,Welfle, H.,Kozerski, C.,Volz, A.,Uchanska-Ziegler, B.,Ziegler, A.
      (2004) J.Biol.Chem. 279: 652


    Organizational Affiliation

    Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
A
276Homo sapiensMutation(s): 0 
Gene Names: HLA-B (HLAB)
Find proteins for P03989 (Homo sapiens)
Go to Gene View: HLA-B
Go to UniProtKB:  P03989
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA-2-MICROGLOBULIN
B
100Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
BUTYRATE RESPONSE FACTOR 2
C
9Homo sapiensMutation(s): 0 
Gene Names: ZFP36L2 (BRF2, ERF2, RNF162C, TIS11D)
Find proteins for P47974 (Homo sapiens)
Go to Gene View: ZFP36L2
Go to UniProtKB:  P47974
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.175α = 90.00
b = 82.670β = 90.00
c = 110.177γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKLdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance