1K5N

HLA-B*2709 BOUND TO NONA-PEPTIDE M9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.123 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 47844-47853

  • DOI: 10.1074/jbc.M206392200
  • Primary Citation of Related Structures:  
    1JGE, 1K5N

  • PubMed Abstract: 
  • The reasons for the association of the human major histocompatibility complex protein HLA-B27 with spondyloarthropathies are unknown. To uncover the underlying molecular causes, we determined the crystal structures of the disease-associated B*2705 an ...

    The reasons for the association of the human major histocompatibility complex protein HLA-B27 with spondyloarthropathies are unknown. To uncover the underlying molecular causes, we determined the crystal structures of the disease-associated B*2705 and the nonassociated B*2709 subtypes complexed with the same nonapeptide (GRFAAAIAK). Both differ in only one residue (Asp(116) and His(116), respectively) in the F-pocket that accommodates the peptide C terminus. Several different effects of the Asp(116) --> His replacement are observed. The bulkier His(116) induces a movement of peptide C-terminal pLys(9), allowing the formation of a novel salt bridge to Asp(77), whereas the salt bridge between pLys(9) and Asp(116) is converted into a hydrogen bond with His(116). His(116) but not Asp(116) adopts two alternative conformations, one of which leads to breakage of hydrogen bonds. Water molecules near residue 116 differ with regard to number, position, and contacts made. Furthermore, F-pocket atoms exhibit higher B-factors in B*2709 than in B*2705, indicating an increased flexibility of the entire region in the former subtype. These changes induce subtle peptide conformational alterations that may be responsible for the immunobiological differences between these HLA-B27 subtypes.


    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
    • 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, Universitätsklinikum 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
major histocompatibility complex molecule HLA-B*2709A276Homo 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-microglobulin, light chainB100Homo 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
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
nonameric model peptide m9C9N/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: 1.09 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.123 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.845α = 90
b = 82.484β = 90
c = 110.708γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-30
    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