Truncated H2-Ld binding "SPSYAYHQF" at 1.80Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Truncated class i with peptide
H2-Ld
SPSYAYHQF
Species
Locus / Allele group
Structures suggest an approach for converting weak self-peptide tumor antigens into superagonists for CD8 T cells in cancer.
Tumors frequently express unmutated self-tumor-associated antigens (self-TAAs). However, trial results using self-TAAs as vaccine targets against cancer are mixed, often attributed to deletion of T cells with high-affinity receptors (TCRs) for self-TAAs during T cell development. Mutating these weak self-TAAs to produce higher affinity, effective vaccines is challenging, since the mutations may not benefit all members of the broad self-TAA-specific T cell repertoire. We previously identified a common weak murine self-TAA that we converted to a highly effective antitumor vaccine by a single amino acid substitution. In this case the modified and natural self-TAAs still raised very similar sets of CD8 T cells. Our structural studies herein show that the modification of the self-TAA resulted in a subtle change in the major histocompatibility complex I-TAA structure. This amino acid substitution allowed a dramatic conformational change in the peptide during subsequent TCR engagement, creating a large increase in TCR affinity and accounting for the efficacy of the modified self-TAA as a vaccine. These results show that carefully selected, well-characterized modifications to a poorly immunogenic self-TAA can rescue the immune response of the large repertoire of weakly responding natural self-TAA-specific CD8 T cells, driving them to proliferate and differentiate into functional effectors. Subsequently, the unmodified self-TAA on the tumor cells, while unable to drive this response, is nevertheless a sufficient target for the CD8 cytotoxic effectors. Our results suggest a pathway for more efficiently identifying variants of common self-TAAs, which could be useful in vaccine development, complementing other current nonantigen-specific immunotherapies.
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
Data provenance
MHC:peptide complexes are visualised using PyMol. The peptide is superimposed on a consistent cutaway slice of the MHC binding cleft (displayed as a grey mesh) which best indicates the binding pockets for the P1/P5/PC positions (side view - pockets A, E, F) and for the P2/P3/PC-2 positions (top view - pockets B, C, D). In some cases peptides will use a different pocket for a specific peptide position (atypical anchoring). On some structures the peptide may appear to sterically clash with a pocket. This is an artefact of picking a standardised slice of the cleft and overlaying the peptide.
Peptide neighbours
P1
SER
TYR171
TYR159
TYR59
TYR7
GLU163
ARG62
ILE66
ILE63
TRP167
MET5
|
P2
PRO
TYR99
TYR45
TYR7
GLU163
ILE66
ILE63
TYR159
|
P3
SER
ARG97
GLN70
GLU114
TYR99
TYR159
GLU9
ILE66
|
P4
TYR
ILE66
GLY69
ARG97
GLN70
TYR155
GLN65
TYR156
|
P5
ALA
TRP73
TYR155
TYR156
PHE116
ARG97
GLN70
|
P6
TYR
GLN70
TRP73
TYR155
TYR156
|
P7
HIS
ALA150
GLY151
ASN77
TRP73
ALA152
TRP147
TYR155
TYR156
|
P8
GLN
TRP147
VAL76
ASN77
LYS146
TRP73
THR143
|
P9
PHE
ASN77
TRP73
TYR84
THR80
LYS146
TRP147
THR143
PHE116
ILE124
LEU81
LEU95
ILE142
TYR123
|
Colour key
Data provenance
Neighbours are calculated by finding residues with atoms within 5Å of each other using BioPython Neighboursearch module. The list of neighbours is then sorted and filtered to inlcude only neighbours where between the peptide and the MHC Class I alpha chain.
Colours selected to match the YRB scheme. [https://www.frontiersin.org/articles/10.3389/fmolb.2015.00056/full]
A Pocket
TYR159
GLU163
TRP167
TYR171
MET5
TYR59
ILE63
ILE66
TYR7
|
B Pocket
SER24
VAL34
TYR45
ILE63
ILE66
ALA67
TYR7
GLN70
GLU9
TYR99
|
C Pocket
GLN70
TRP73
PHE74
GLU9
ARG97
|
D Pocket
GLU114
TYR155
TYR156
TYR159
LEU160
TYR99
|
E Pocket
GLU114
TRP147
ALA152
TYR156
ARG97
|
F Pocket
PHE116
TYR123
THR143
LYS146
TRP147
ASN77
THR80
LEU81
TYR84
LEU95
|
Colour key
Data provenance
1. Class I alpha
H2-Ld
|
10 20 30 40 50 60
GPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEYW 70 80 90 100 110 120 ERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYDG 130 140 150 160 170 CDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNG |
2. Peptide
|
SPSYAYHQF
|
Data provenance
Sequences are retrieved via the Uniprot method of the RSCB REST API. Sequences are then compared to those derived from the PDB file and matched against sequences retrieved from the IPD-IMGT/HLA database for human sequences, or the IPD-MHC database for other species. Mouse sequences are matched against FASTA files from Uniprot. Sequences for the mature extracellular protein (signal petide and cytoplasmic tail removed) are compared to identical length sequences from the datasources mentioned before using either exact matching or Levenshtein distance based matching.
Downloadable data
Components
Data license
Footnotes
- Protein Data Bank Europe - Coordinate Server
- 1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
- Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
- PyMol - PyMol.org/pymol
- Levenshtein distance - Wikipedia entry
- Protein Data Bank Europe REST API - Molecules endpoint
- 3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
- Protein Data Bank Europe REST API - Publication endpoint
- PubMed Central Europe REST API - Articles endpoint
This work is licensed under a Creative Commons Attribution 4.0 International License.