Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

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

Macromolecule Content

• Total Structure Weight: 94.10 kDa 
• Atom Count: 7153 
• Residue Count: 829 
• Unique protein chains: 5

2BNQ

Structural and kinetic basis for heightened immunogenicity of T cell vaccines

• DOI: 10.2210/pdb2BNQ/pdb

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


• Deposited: 2005-03-31 Released: 2005-05-23 
• Deposition Author(s): Chen, J.-L., Stewart-Jones, G., Bossi, G., Lissin, N.M., Wooldridge, L., Choi, E.M.L., Held, G., Dunbar, P.R., Esnouf, R.M., Sami, M., Boultier, J.M., Rizkallah, P.J., Renner, C., Sewell, A., van der Merwe, P.A., Jackobsen, B.K., Griffiths, G., Jones, E.Y., Cerundolo, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.253 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

Structural and Kinetic Basis for Heightened Immunogenicity of T Cell Vaccines

Chen, J.-L., Stewart-Jones, G., Bossi, G., Lissin, N.M., Wooldridge, L., Choi, E.M.L., Held, G., Dunbar, P.R., Esnouf, R.M., Sami, M., Boultier, J.M., Rizkallah, P., Renner, C., Sewell, A., Van Der Merwe, P.A., Jackobsen, B.K., Griffiths, G., Jones, E.Y., Cerundolo, V.

(2005) J Exp Med 201: 1243

• PubMed: 15837811 
• DOI: 10.1084/jem.20042323
• Primary Citation of Related Structures:  
  2BNU, 2BNR, 2BNQ


• PubMed Abstract: 
  

Analogue peptides with enhanced binding affinity to major histocompatibility class (MHC) I molecules are currently being used in cancer patients to elicit stronger T cell responses. However, it remains unclear as to how alterations of anchor residues may affect T cell receptor (TCR) recognition. We correlate functional, thermodynamic, and structural parameters of TCR-peptide-MHC binding and demonstrate the effect of anchor residue modifications of the human histocompatibility leukocyte antigens (HLA)-A2 tumor epitope NY-ESO-1(157-165)-SLLMWITQC on TCR recognition. The crystal structure of the wild-type peptide complexed with a specific TCR shows that TCR binding centers on two prominent, sequential, peptide sidechains, methionine-tryptophan. Cysteine-to-valine substitution at peptide position 9, while optimizing peptide binding to the MHC, repositions the peptide main chain and generates subtly enhanced interactions between the analogue peptide and the TCR. Binding analyses confirm tighter binding of the analogue peptide to HLA-A2 and improved soluble TCR binding. Recognition of analogue peptide stimulates faster polarization of lytic granules to the immunological synapse, reduces dependence on CD8 binding, and induces greater numbers of cross-reactive cytotoxic T lymphocyte to SLLMWITQC. These results provide important insights into heightened immunogenicity of analogue peptides and highlight the importance of incorporating structural data into the process of rational optimization of superagonist peptides for clinical trials.

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Related Citations: 

• Identification of NY-Eso-1 Peptide Analogues Capable of Improved Stimulation of Tumor-Reactive Ctl
  Chen, J.-L., Dunbar, P.R., Gileadi, U., Jager, E., Gnjatic, S., Nagata, Y., Stockert, E., Panicali, D.L., Chen, Y.-T., Knuth, A., Old, L.J., Cerundolo, V.
  (2000) J Immunol 165: 948

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Organizational Affiliation: 

Tumour Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA CLASS I HISTOCOMPATIBILITY ANTIGEN	A	276	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	100	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
SYNTHETIC PEPTIDE	C	9	Homo sapiens	Mutation(s): 0  Gene Names: CTAG1A, CTAG, CTAG1, ESO1, LAGE2, LAGE2A, CTAG1B, LAGE2B
Find proteins for P78358 (Homo sapiens) Explore P78358  Go to UniProtKB:  P78358
NIH Common Fund Data Resources
PHAROS:  P78358 GTEx:  ENSG00000184033ENSG00000268651

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T-CELL RECEPTOR ALPHA CHAIN V REGION	D	203	Homo sapiens	Mutation(s): 0  Gene Names: TRAC, TCRA, TRAV21
Find proteins for P01848 (Homo sapiens) Explore P01848  Go to UniProtKB:  P01848
NIH Common Fund Data Resources
PHAROS:  P01848
Find proteins for A0A0B4J279 (Homo sapiens) Explore A0A0B4J279  Go to UniProtKB:  A0A0B4J279
NIH Common Fund Data Resources
PHAROS:  A0A0B4J279 GTEx:  ENSG00000211801

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T-CELL RECEPTOR BETA CHAIN C REGION	E	241	Homo sapiens	Mutation(s): 0  Gene Names: TRBC1, TRBV6-5
Find proteins for A0A0K0K1A5 (Homo sapiens) Explore A0A0K0K1A5  Go to UniProtKB:  A0A0K0K1A5
NIH Common Fund Data Resources
PHAROS:  A0A0K0K1A5 GTEx:  ENSG00000211721
Find proteins for P01850 (Homo sapiens) Explore P01850  Go to UniProtKB:  P01850

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.253 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.563	α = 90
b = 62.49	β = 105.34
c = 116.955	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-03-31 
• Released Date: 2005-05-23 
Deposition Author(s): Chen, J.-L., Stewart-Jones, G., Bossi, G., Lissin, N.M., Wooldridge, L., Choi, E.M.L., Held, G., Dunbar, P.R., Esnouf, R.M., Sami, M., Boultier, J.M., Rizkallah, P.J., Renner, C., Sewell, A., van der Merwe, P.A., Jackobsen, B.K., Griffiths, G., Jones, E.Y., Cerundolo, V.

Revision History 

• Version 1.0: 2005-05-23
  Type: Initial release
  
• Version 1.1: 2015-11-25
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance