1JGD

HLA-B*2709 bound to deca-peptide s10R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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
  • Primary Citation of Related Structures:  
    1JGD

  • 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 differentially disease-associated subtypes HLA-B*2705 and HLA-B*2709 was carried out ...

    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: 
    • 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
    • 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
    • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN LYMPHOCYTE ANTIGEN HLA-B27A276Homo sapiensMutation(s): 0 
Gene Names: HLA-B or HLABHLA-BHLAB
Find proteins for P01889 (Homo sapiens)
Explore P01889 
Go to UniProtKB:  P01889
NIH Common Fund Data Resources
PHAROS  P01889
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-2-MICROGLOBULINB100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
peptide s10RC10N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.844α = 90
b = 48.438β = 121.291
c = 88.532γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

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