6SS9 image
Entry Detail
PDB ID:
6SS9
Keywords:
Title:
Human Leukocyte Antigen Class I A02 Carrying LLWNGPMHV
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2019-09-06
Release Date:
2020-07-15
Method Details:
Experimental Method:
Resolution:
2.70 Å
R-Value Free:
0.30
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:HLA class I histocompatibility antigen, A-2 alpha chain
Chain IDs:A, D
Chain Length:276
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Beta-2-microglobulin
Chain IDs:B, E
Chain Length:100
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:LEU-LEU-TRP-ASN-GLY-PRO-MET-HIS-VAL
Chain IDs:C, F
Chain Length:9
Number of Molecules:2
Biological Source:Yellow fever virus
Primary Citation
Identification of a superagonist variant of the immunodominant Yellow fever virus epitope NS4b214-222by combinatorial peptide library screening.
Mol.Immunol. 125 43 50 (2020)
PMID: 32645549 DOI: 10.1016/j.molimm.2020.06.025

Abstact

The CD8 T cell response to the HLA-A2-restricted epitope LLWNGPMAV (LLW) of the non-structural protein 4b of Yellow Fever Virus (YFV) is remarkably immunodominant, highly prevalent and powerful in YFV-vaccinated humans. Here we used a combinatorial peptide library screening in the context of an A2/LLW-specific CD8 T cell clone to identify a superagonist that features a methionine to isoleucine substitution at position 7. Based on in silico modeling, the functional enhancement of this LLW-7I mutation was associated with alterations in the structural dynamics of the peptide in the major histocompatibility complex (pMHC) binding with the T cell receptor (TCR). While the TCR off-rate of LLW-7I pMHC is comparable to the wild type peptide, the rigidity of the 7I peptide seems to confer less entropy loss upon TCR binding. This LLW-7I superagonist is an example of improved functionality in human CD8 T cells associated with optimized ligand rigidity for TCR binding and not with changes in TCR:pMHC off-rate kinetics.

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