Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 

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

Macromolecule Content

• Total Structure Weight: 90.63 kDa 
• Atom Count: 7465 
• Residue Count: 770 
• Unique protein chains: 3

4WJ5

Structure of HLA-A2 in complex with an altered peptide ligands based on Mart-1 variant epitope

• DOI: 10.2210/pdb4WJ5/pdb

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


• Deposited: 2014-09-29 Released: 2014-10-29 
• Deposition Author(s): Celie, P.H.N., Rodenko, B., Ovaa, H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.179 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

Literature

Altered Peptide Ligands Revisited: Vaccine Design through Chemically Modified HLA-A2-Restricted T Cell Epitopes.

Hoppes, R., Oostvogels, R., Luimstra, J.J., Wals, K., Toebes, M., Bies, L., Ekkebus, R., Rijal, P., Celie, P.H., Huang, J.H., Emmelot, M.E., Spaapen, R.M., Lokhorst, H., Schumacher, T.N., Mutis, T., Rodenko, B., Ovaa, H.

(2014) J Immunol 193: 4803-4813

• PubMed: 25311806 
• DOI: 10.4049/jimmunol.1400800
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Virus or tumor Ag-derived peptides that are displayed by MHC class I molecules are attractive starting points for vaccine development because they induce strong protective and therapeutic cytotoxic T cell responses. In thus study, we show that the MHC binding and consequent T cell reactivity against several HLA-A*02 restricted epitopes can be further improved through the incorporation of nonproteogenic amino acids at primary and secondary anchor positions. We screened more than 90 nonproteogenic, synthetic amino acids through a range of epitopes and tested more than 3000 chemically enhanced altered peptide ligands (CPLs) for binding affinity to HLA-A*0201. With this approach, we designed CPLs of viral epitopes, of melanoma-associated Ags, and of the minor histocompatibility Ag UTA2-1, which is currently being evaluated for its antileukemic activity in clinical dendritic cell vaccination trials. The crystal structure of one of the CPLs in complex with HLA-A*0201 revealed the molecular interactions likely responsible for improved binding. The best CPLs displayed enhanced affinity for MHC, increasing MHC stability and prolonging recognition by Ag-specific T cells and, most importantly, they induced accelerated expansion of antitumor T cell frequencies in vitro and in vivo as compared with the native epitope. Eventually, we were able to construct a toolbox of preferred nonproteogenic residues with which practically any given HLA-A*02 restricted epitope can be readily optimized. These CPLs could improve the therapeutic outcome of vaccination strategies or can be used for ex vivo enrichment and faster expansion of Ag-specific T cells for transfer into patients.

---

Organizational Affiliation: 

Division of Cell Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands;

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Beta-2-microglobulin	B, E	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Go to UniProtKB:  P61769
NIH Common Fund Data Resources
PHAROS  P61769 GTEx  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Melanoma antigen recognized by T-cells 1	C, F	10	Homo sapiens	Mutation(s): 0  Gene Names: MLANA, MART1
Find proteins for Q16655 (Homo sapiens) Go to UniProtKB:  Q16655
NIH Common Fund Data Resources
PHAROS  Q16655 GTEx  ENSG00000120215

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A, B, D, E	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NVA	C,F	L-PEPTIDE LINKING	C5 H11 N O2		VAL

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.179 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.18	α = 90
b = 87.14	β = 90.15
c = 79.194	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
XDS	data reduction
PDB_EXTRACT	data extraction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-09-29 
• Released Date: 2014-10-29 
Deposition Author(s): Celie, P.H.N., Rodenko, B., Ovaa, H.

Revision History 

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Database references