1HHI

THE ANTIGENIC IDENTITY OF PEPTIDE(SLASH)MHC COMPLEXES: A COMPARISON OF THE CONFORMATION OF FIVE PEPTIDES PRESENTED BY HLA-A2

• PDB DOI:  https://doi.org/10.2210/pdb1HHI/pdb

• Classification: HISTOCOMPATIBILITY ANTIGEN
• Organism(s): Homo sapiens, Influenza A virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1993-06-30 Released: 1993-10-31 
• Deposition Author(s): Madden, D.R., Garboczi, D.N., Wiley, D.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.273 
• R-Value Observed: 0.273 

Literature

The antigenic identity of peptide-MHC complexes: a comparison of the conformations of five viral peptides presented by HLA-A2.

Madden, D.R., Garboczi, D.N., Wiley, D.C.

(1993) Cell 75: 693-708

• PubMed: 7694806 
• DOI: https://doi.org/10.1016/0092-8674(93)90490-h
• Primary Citation of Related Structures:  
  1HHG, 1HHH, 1HHI, 1HHJ, 1HHK


• PubMed Abstract: 
  

Complexes of five peptides (from HIV-1, influenza A virus, HTLV-1, and hepatitis B virus proteins) bound to the human class I MHC molecule HLA-A2 have been studied by X-ray crystallography. While the peptide termini and their second and C-terminal anchor side chains are bound similarly in all five cases, the main chain and side chain conformations of each peptide are strikingly different in the center of the binding site, and these differences are accessible to direct TCR recognition. Each of the central peptide residues is seen to point up for some bound peptides, but down or sideways for others. Thus, although fixed at its ends, the structure of an MHC-bound peptide appears to be a highly complex function of its entire sequence, potentially sensitive to even small sequence differences. In contrast, MHC structural variation is relatively limited. These results offer a structural framework for understanding the role of nonanchor peptide side chains in both peptide-MHC binding affinity and TCR recognition.

---

Related Citations: 

• Hla-A2-Peptide Complexes: Refolding and Crystallization of Molecules Expressed in Escherichia Coli and Complexed with Single Antigenic Peptides
  Garboczi, D.N., Hung, D.T., Wiley, D.C.
  (1992) Proc Natl Acad Sci U S A 89: 3429

• The Minimum Peptide Epitope from the Influenza Virus Matrix Protein
  Bednarek, M.A., Sauma, S.Y., Gammon, M.C., Porter, G., Tamhankar, S., Williamson, A.R., Zweerink, H.J.
  (1991) J Immunol 147: 4047

• Identification of the Nonamer Peptide from Influenza a Matrix Protein and the Role of Pockets of Hla-A2 in its Recognition by Cytotoxic T Lymphocytes
  Morrison, J., Elvin, J., Latron, F., Gotch, F., Moots, R., Strominger, J.L., Mcmichael, A.
  (1992) Eur J Immunol 22: 903

• The Three-Dimensional Structure of Hla-B27 at 2.1 Angstroms 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

• Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution
  Saper, M.A., Bjorkman, P.J., Wiley, D.C.
  (1991) J Mol Biol 219: 277

• 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

---

Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.4 kDa 
• Atom Count: 6,306 
• Modelled Residue Count: 768 
• Deposited Residue Count: 768 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A*0201) (ALPHA CHAIN)	A, D	275	Homo sapiens	Mutation(s): 0  Gene Names: BETA-2-MICROGLOBULIN, HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA 2-MICROGLOBULIN	B, E	100	Homo sapiens	Mutation(s): 0  Gene Names: BETA-2-MICROGLOBULIN, B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
INFLUENZA A MATRIX PROTEIN M1 (RESIDUES 58-66)	C, F	9	Influenza A virus	Mutation(s): 0
UniProt
Find proteins for P03485 (Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)) Explore P03485  Go to UniProtKB:  P03485

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.273 
• R-Value Observed: 0.273 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.35	α = 90
b = 87.71	β = 90.1
c = 79.22	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Madden, D.R., Garboczi, D.N., Wiley, D.C.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance