2HLA

SPECIFICITY POCKETS FOR THE SIDE CHAINS OF PEPTIDE ANTIGENS IN HLA-AW68

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Specificity pockets for the side chains of peptide antigens in HLA-Aw68.

Garrett, T.P., Saper, M.A., Bjorkman, P.J., Strominger, J.L., Wiley, D.C.

(1989) Nature 342: 692-696

  • DOI: 10.1038/342692a0

  • PubMed Abstract: 

    • We have determined the structure of a second human histocompatibility glycoprotein, HLA-Aw68, by X-ray crystallography and refined it to a resolution of 2.6 A. Overall, the structure is extremely similar to that of HLA-A2 (refs 1, 2; and M.A.S. et al ...

    We have determined the structure of a second human histocompatibility glycoprotein, HLA-Aw68, by X-ray crystallography and refined it to a resolution of 2.6 A. Overall, the structure is extremely similar to that of HLA-A2 (refs 1, 2; and M.A.S. et al., manuscript in preparation), although the 11 amino-acid substitutions at polymorphic residues in the antigen-binding cleft alter the detailed shape and electrostatic charge of that site. A prominent negatively charged pocket within the cleft extends underneath the alpha-helix of the alpha 1-domain, providing a potential subsite for recognizing a positively charged side chain or peptide N terminus. Uninterpreted electron density, presumably representing an unknown 'antigen(s)', which seems to be different from that seen in the HLA-A2 structure, occupies the cleft and extends into the negatively charged pocket in HLA-Aw68. The structures of HLA-Aw68 and HLA-A2 demonstrate how polymorphism creates and alters subsites (pockets) positioned to bind peptide side chains, thereby suggesting the structural basis for allelic specificity in foreign antigen binding.

    Related Citations: 
    • Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes
      Bjorkman, P.J.,Strominger, J.L.,Wiley, D.C.
      (1985) J.Mol.Biol. 186: 205
    • Garrett, T.P.J.,Saper, M.A.,Wiley, D.C.
      () TO BE PUBLISHED --: --
    • Structure of the Human Class I Histocompatibility Antigen, Hla-A2
      Bjorkman, P.J.,Saper, M.A.,Samraoui, B.,Bennett, W.S.,Strominger, J.L.,Wiley, D.C.
      (1987) Nature 329: 506
    • The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens
      Bjorkman, P.J.,Saper, M.A.,Samraoui, B.,Bennett, W.S.,Strominger, J.L.,Wiley, D.C.
      (1987) Nature 329: 512

    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-Aw68)
A
270Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P01891 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P01891
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BETA 2-MICROGLOBULIN
B
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Work: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.000α = 90.00
b = 80.660β = 90.00
c = 113.000γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1990-04-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other