1JGD

HLA-B*2709 bound to deca-peptide s10R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Thermodynamic and structural analysis of peptide- and allele-dependent properties of two HLA-B27 subtypes exhibiting differential disease association

Hillig, R.C.Huelsmeyer, M.Saenger, W.Welfle, K.Misselwitz, R.Welfle, H.Kozerski, C.Volz, A.Uchanska-Ziegler, B.Ziegler, A.

(2004) J.Biol.Chem. 279: 652-663

  • DOI: 10.1074/jbc.M307457200
  • Also Cited By: 1W0V, 1W0W

  • PubMed Abstract: 
  • Selected HLA-B27 subtypes are associated with spondyloarthropathies, but the underlying mechanism is not understood. To explain this association in molecular terms, a comparison of peptide-dependent dynamic and structural properties of the differenti ...

    Selected HLA-B27 subtypes are associated with spondyloarthropathies, but the underlying mechanism is not understood. To explain this association in molecular terms, a comparison of peptide-dependent dynamic and structural properties of the differentially disease-associated subtypes HLA-B*2705 and HLA-B*2709 was carried out. These molecules differ only by a single amino acid at the floor of the peptide binding groove. The thermostabilities of a series of HLA-B27 molecules complexed with nonameric and decameric peptides were determined and revealed substantial differences depending on the subtype as well as the residues at the termini of the peptides. In addition we present the crystal structure of the B*2709 subtype complexed with a decameric peptide. This structure provides an explanation for the preference of HLA-B27 for a peptide with an N-terminal arginine as secondary anchor and the lack of preference for tyrosine as peptide C terminus in B*2709. The data show that differences in thermodynamic properties between peptide-complexed HLA-B27 subtypes are correlated with a variety of structural properties.


    Related Citations: 
    • Identification of a Novel HLA-B27 Subtype by Restriction Analysis of a Cytotoxic gamma delta T Cell Clone
      Del Porto, P.,D'Amato, M.,Fiorillo, M.T.,Tuosto, L.,Piccolella, E.,Sorrention, R.
      (1994) J.IMMUNOL. 153: 3093
    • HLA-B27 subtypes differentially associated with disease exhibit subtle structural alterations
      Hulsmeyer, M.,Hillig, R.C.,Volz, A.,Ruhl, M.,Schroder, W.,Saenger, W.,Ziegler, A.,Uchanska-Ziegler, B.
      (2002) J.Biol.Chem. 277: 47844
    • The Structure of HLA-B27 Reveals Nonamer Self-peptides Bound in an Extended Conformation
      Madden, D.R.,Gorga, J.C.,Strominger, J.L.,Wiley, D.C.
      (1991) Nature 353: 321
    • The Three-dimensional Structure of HLA-B27 at 2.1 A Resolution Suggests a General Mechanism for Tight Peptide Binding to MHC
      Madden, D.R.,Gorga, J.C.,Strominger, J.L.,Wiley, D.C.
      (1992) Cell 70: 1035


    Organizational Affiliation

    Institut für Immungenetik, Charité, Humboldt-Universität zu Berlin, Spandauer Damm 130, 14050 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN LYMPHOCYTE ANTIGEN HLA-B27
A
276Homo sapiensGene 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 sapiensGene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
peptide s10R
C
10N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
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: 1.9 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 129.844α = 90.00
b = 48.438β = 121.29
c = 88.532γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-24
    Type: Database references