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)

Biological Assembly 2  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 89.32 kDa 
• Atom Count: 6417 
• Residue Count: 766 
• Unique protein chains: 3

3CPL

Crystal Structure of H-2Db in complex with a variant M6A of the NP366 peptide from influenza A virus

• DOI: 10.2210/pdb3CPL/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-31 Released: 2008-11-18 
• Deposition Author(s): Kedzierska, K., Guillonneau, C., Hatton, L.A., Stockwell, D., Gras, S., Webby, R., Rossjohn, J., Purcell, A.W., Doherty, P.C., Turner, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.286 
• R-Value Work: 0.220 
• R-Value Observed: 0.227 

Literature

Complete modification of TCR specificity and repertoire selection does not perturb a CD8+ T cell immunodominance hierarchy.

Kedzierska, K., Guillonneau, C., Gras, S., Hatton, L.A., Webby, R., Purcell, A.W., Rossjohn, J., Doherty, P.C., Turner, S.J.

(2008) Proc Natl Acad Sci U S A 105: 19408-19413

• PubMed: 19047637 
• DOI: 10.1073/pnas.0810274105
• Primary Citation of Related Structures:  
  3CPL


• PubMed Abstract: 
  

Understanding T cell immunodominance hierarchies is fundamental to the development of cellular-based vaccines and immunotherapy. A combination of influenza virus infection in C57BL/6J mice and reverse genetics is used here to dissect the role of T cell antigen receptor (TCR) repertoire in the immunodominant D(b)NP(366)CD8(+) T cell response. Infection with an engineered virus (NPM6A) containing a single alanine (A) mutation at the critical p6 NP(366-374) residue induced a noncross-reactive CD8(+) T cell response characterized by a novel, narrower TCR repertoire per individual mouse that was nonetheless equivalent in magnitude to that generated after WT virus challenge. Although of lower overall avidity, the levels of both cytotoxic T lymphocyte activity and cytokine production were comparable with those seen for the native response. Importantly, the overdominance profile characteristic of secondary D(b)NP(366)-specific clonal expansions was retained for the NPM6A mutant. The primary determinants of immunodominance in this endogenous, non-TCR-transgenic model of viral immunity are thus independent of TCR repertoire composition and diversity. These findings both highlight the importance of effective antigen dose for T cell vaccination and/or immunotherapy and demonstrate the feasibility of priming the memory T cell compartment with engineered viruses to protect against commonly selected mutants viral (or tumor) escape mutants.

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Organizational Affiliation: 

Department of Microbiology and Immunology, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville 3010, Melbourne, Australia. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, D-B alpha chain	A, C	275	Mus musculus	Mutation(s): 0  Gene Names: H2-D1
Find proteins for P01899 (Mus musculus) Explore P01899  Go to UniProtKB:  P01899

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D	99	Mus musculus	Mutation(s): 0  Gene Names: B2m
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NP366 peptide	E, F	9	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.286 
• R-Value Work: 0.220 
• R-Value Observed: 0.227 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.71	α = 99.95
b = 69.7	β = 111.04
c = 72.38	γ = 110.48

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-31 
• Released Date: 2008-11-18 
Deposition Author(s): Kedzierska, K., Guillonneau, C., Hatton, L.A., Stockwell, D., Gras, S., Webby, R., Rossjohn, J., Purcell, A.W., Doherty, P.C., Turner, S.J.

Revision History 

• Version 1.0: 2008-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance