Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.90 kDa 
• Atom Count: 3033 
• Residue Count: 369 
• Unique protein chains: 2

2HLA

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

• DOI: 10.2210/pdb2HLA/pdb

• Classification: HISTOCOMPATIBILITY ANTIGEN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1989-10-05 Released: 1990-04-15 
• Deposition Author(s): Garrett, T.P.J., Saper, M.A., Wiley, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.173 

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

• PubMed: 2594067 
• DOI: 10.1038/342692a0
• Primary Citation of Related Structures:  
  2HLA


• 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., 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.

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Related Citations: 

• 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

• 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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-Aw68)	A	270	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
NIH Common Fund Data Resources
PHAROS  P04439 GTEx  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA 2-MICROGLOBULIN	B	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Work: 0.173 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60	α = 90
b = 80.66	β = 90
c = 113	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1989-10-05 
• Released Date: 1990-04-15 
Deposition Author(s): Garrett, T.P.J., Saper, M.A., Wiley, D.C.

Revision History 

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