Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 44.91 kDa 
• Atom Count: 3707 
• Modelled Residue Count: 385 
• Deposited Residue Count: 385 
• Unique protein chains: 3

2AXF

The Immunogenicity of a Viral Cytotoxic T Cell Epitope is controlled by its MHC-bound Conformation

• DOI: 10.2210/pdb2AXF/pdb

• Classification: IMMUNE SYSTEM/GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-09-05 Released: 2005-11-29 
• Deposition Author(s): Tynan, F.E., Elhassen, D., Purcell, A.W., Burrows, J.M., Borg, N.A., Miles, J.J., Williamson, N.A., Green, K.J., Tellam, J., Kjer-Nielsen, L., McCluskey, J., Rossjohn, J., Burrows, S.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

Literature

The immunogenicity of a viral cytotoxic T cell epitope is controlled by its MHC-bound conformation

Tynan, F.E., Elhassen, D., Purcell, A.W., Burrows, J.M., Borg, N.A., Miles, J.J., Williamson, N.A., Green, K.J., Tellam, J., Kjer-Nielsen, L., McCluskey, J., Rossjohn, J., Burrows, S.R.

(2005) J Exp Med 202: 1249-1260

• PubMed: 16275762 
• DOI: 10.1084/jem.20050864
• Primary Citation of Related Structures:  
  2AXG, 2AXF


• PubMed Abstract: 
  

Thousands of potentially antigenic peptides are encoded by an infecting pathogen; however, only a small proportion induce measurable CD8(+) T cell responses. To investigate the factors that control peptide immunogenicity, we have examined the cytotoxic T lymphocyte (CTL) response to a previously undefined epitope ((77)APQPAPENAY(86)) from the BZLF1 protein of Epstein-Barr virus (EBV). This peptide binds well to two human histocompatibility leukocyte antigen (HLA) allotypes, HLA-B*3501 and HLA-B*3508, which differ by a single amino acid at position 156 ((156)Leucine vs. (156)Arginine, respectively). Surprisingly, only individuals expressing HLA-B*3508 show evidence of a CTL response to the (77)APQPAPENAY(86) epitope even though EBV-infected cells expressing HLA-B*3501 process and present similar amounts of peptide for CTL recognition, suggesting that factors other than peptide presentation levels are influencing immunogenicity. Functional and structural analysis revealed marked conformational differences in the peptide, when bound to each HLA-B35 allotype, that are dictated by the polymorphic HLA residue 156 and that directly affected T cell receptor recognition. These data indicate that the immunogenicity of an antigenic peptide is influenced not only by how well the peptide binds to major histocompatibility complex (MHC) molecules but also by its bound conformation. It also illustrates a novel mechanism through which MHC polymorphism can further diversify the immune response to infecting pathogens.

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Organizational Affiliation: 

The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B*3508 heavy chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
PHAROS:  P01889 GTEx:  ENSG00000234745

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
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
10-mer peptide from BZLF1 trans-activator protein	C	10	N/A	Mutation(s): 0
UniProt
Find proteins for P03206 (Epstein-Barr virus (strain B95-8)) Explore P03206  Go to UniProtKB:  P03206

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	D [auth A], E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.825	α = 90
b = 81.528	β = 90
c = 110.732	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-05 
• Released Date: 2005-11-29 
Deposition Author(s): Tynan, F.E., Elhassen, D., Purcell, A.W., Burrows, J.M., Borg, N.A., Miles, J.J., Williamson, N.A., Green, K.J., Tellam, J., Kjer-Nielsen, L., McCluskey, J., Rossjohn, J., Burrows, S.R.

Revision History  

• Version 1.0: 2005-11-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description