3REW | pdb_00003rew

Crystal structure of an lmp2a-derived peptide bound to human class i mhc hla-a2

• PDB DOI: https://doi.org/10.2210/pdb3REW/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Human herpesvirus 4 strain B95-8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-05 Released: 2012-01-18 
• Deposition Author(s): Wood, A., Mohammed, F., Salim, M., Tranter, A., Rickinson, A.B., Moss, P.A.H., Stauss, H.J., Steven, N.M., Willcox, B.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.239 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.208 (Depositor) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structural and energetic evidence for highly peptide-specific tumor antigen targeting via allo-MHC restriction.

Simpson, A.A., Mohammed, F., Salim, M., Tranter, A., Rickinson, A.B., Stauss, H.J., Moss, P.A., Steven, N.M., Willcox, B.E.

(2011) Proc Natl Acad Sci U S A 108: 21176-21181

• PubMed: 22160697 
• DOI: https://doi.org/10.1073/pnas.1108422109
• Primary Citation Related Structures: 
  3REV, 3REW


• PubMed Abstract: 
  

  Immunotherapies targeting peptides presented by allogeneic MHC molecules offer the prospect of circumventing tolerance to key tumor-associated self-antigens. However, the degree of antigen specificity mediated by alloreactive T cells, and their ability to discriminate normal tissues from transformed cells presenting elevated antigen levels, is poorly understood. We examined allorecognition of an HLA-A2-restricted Hodgkin's lymphoma-associated antigen and were able to isolate functionally antigen-specific allo-HLA-A2-restricted T cells from multiple donors. Binding and structural studies, focused on a prototypic allo-HLA-A2-restricted T-cell receptor (TCR) termed NB20 derived from an HLA-A3 homozygote, suggested highly peptide-specific allorecognition that was energetically focused on antigen, involving direct recognition of a distinct allopeptide presented within a conserved MHC recognition surface. Although NB20/HLA-A2 affinity was unremarkable, TCR/MHC complexes were very short-lived, consistent with suboptimal TCR triggering and tolerance to low antigen levels. These data provide strong molecular evidence that within the functionally heterogeneous alloreactive repertoire, there is the potential for highly antigen-specific "allo-MHC-restricted" recognition and suggest a kinetic mechanism whereby allo-MHC-restricted T cells may discriminate normal from transformed tissue, thereby outlining a suitable basis for broad-based therapeutic targeting of tolerizing tumor antigens.

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Organizational Affiliation: 
• Birmingham Cancer Research UK Cancer Centre, School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom.

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: 90.33 kDa 
• Atom Count: 6,699 
• Modeled Residue Count: 758 
• Deposited Residue Count: 766 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A, D	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439 GTEx:  ENSG00000206503

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	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
Latent membrane protein 2	C, F	9	Human herpesvirus 4 strain B95-8	Mutation(s): 0
UniProt
Find proteins for P13285 (Epstein-Barr virus (strain B95-8)) Explore P13285  Go to UniProtKB:  P13285

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	G [auth A], H [auth A], I [auth A], K [auth B], N [auth C], O [auth D], R [auth E], U [auth F]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO	J [auth A], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	L [auth B], P [auth D], Q [auth D], S [auth E], T [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.239 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.208 (Depositor) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.75	α = 90
b = 141.44	β = 90
c = 141.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-18 
Deposition Author(s): Wood, A., Mohammed, F., Salim, M., Tranter, A., Rickinson, A.B., Moss, P.A.H., Stauss, H.J., Steven, N.M., Willcox, B.E.

Revision History  

• Version 1.0: 2012-01-18
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.3: 2023-09-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-27
  Changes: Structure summary