Biological Assembly 1  

 3D View: Structure | Electron Density

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: 44.90 kDa 
• Atom Count: 3560 
• Residue Count: 386 
• Unique protein chains: 3

1ZSD

Crystal Structure Of HLA-B*3501 Presenting an 11-Mer EBV Antigen EPLPQGQLTAY

• DOI: 10.2210/pdb1ZSD/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-05-24 Released: 2005-06-07 
• Deposition Author(s): Miles, J.J., Elhassen, D., Borg, N.A., Silins, S.L., Tynan, F.E., Burrows, J.M., Purcell, A.W., Kjer-Nielsen, L., Rossjohn, J., Burrows, S.R., McCluskey, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.246 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 

Literature

CTL Recognition of a Bulged Viral Peptide Involves Biased TCR Selection.

Miles, J.J., Elhassen, D., Borg, N.A., Silins, S.L., Tynan, F.E., Burrows, J.M., Purcell, A.W., Kjer-Nielsen, L., Rossjohn, J., Burrows, S.R., McCluskey, J., El-Hassen, D.

(2005) J Immunol 175: 3826-3834

• PubMed: 16148129 
• DOI: 10.4049/jimmunol.175.6.3826
• Primary Citation of Related Structures:  
  1ZSD


• PubMed Abstract: 
  

MHC class I molecules generally present peptides of 8-10 aa long, forming an extended coil in the HLA cleft. Although longer peptides can also bind to class I molecules, they tend to bulge from the cleft and it is not known whether the TCR repertoire has sufficient plasticity to recognize these determinants during the antiviral CTL response. In this study, we show that unrelated individuals infected with EBV generate a significant CTL response directed toward an HLA-B*3501-restricted, 11-mer epitope from the BZLF1 Ag. The 11-mer determinant adopts a highly bulged conformation with seven of the peptide side chains being solvent-exposed and available for TCR interaction. Such a complex potentially creates a structural challenge for TCR corecognition of both HLA-B*3501 and the peptide Ag. Surprisingly, unrelated B*3501 donors recognizing the 11-mer use identical or closely related alphabeta TCR sequences that share particular CDR3 motifs. Within the small number of dominant CTL clonotypes observed, each has discrete fine specificity for the exposed side chain residues of the peptide. The data show that bulged viral peptides are indeed immunogenic but suggest that the highly constrained TCR repertoire reflects a limit to TCR diversity when responding to some unusual MHC peptide ligands.

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Organizational Affiliation: 

Cellular Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B-35 alpha chain	A	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLAB
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
NIH Common Fund Data Resources
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
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BZLF1 trans-activator protein	C	11	N/A	Mutation(s): 0
Find proteins for P03206 (Epstein-Barr virus (strain B95-8)) Explore P03206  Go to UniProtKB:  P03206

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.246 
• R-Value Work: 0.219 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.93	α = 90
b = 81.49	β = 90
c = 109.92	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-24 
• Released Date: 2005-06-07 
Deposition Author(s): Miles, J.J., Elhassen, D., Borg, N.A., Silins, S.L., Tynan, F.E., Burrows, J.M., Purcell, A.W., Kjer-Nielsen, L., Rossjohn, J., Burrows, S.R., McCluskey, J.

Revision History 

• Version 1.0: 2005-06-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2018-01-31
  Changes: Experimental preparation