Truncated H2-Ld presenting "QLSPFPFDL" to Alpha/Beta T cell receptor at 2.50Å 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 and alpha beta tcr
H2-Ld
QLSPFPFDL
TRAV9
TRBV13
Species
Locus / Allele group
How a single T cell receptor recognizes both self and foreign MHC.
alphabeta T cell receptors (TCRs) can crossreact with both self- and foreign- major histocompatibility complex (MHC) proteins in an enigmatic phenomenon termed alloreactivity. Here we present the 2.35 A structure of the 2C TCR complexed with its foreign ligand H-2L(d)-QL9. Surprisingly, we find that this TCR utilizes a different strategy to engage the foreign pMHC in comparison to the manner in which it recognizes a self ligand H-2K(b)-dEV8. 2C engages both shared and polymorphic residues on L(d) and K(b), as well as the unrelated QL9 and dEV8 peptide antigens, in unique pair-wise contacts, resulting in greater structural complementarity with the L(d)-QL9 complex. In the structure of an engineered, high-affinity 2C TCR variant bound to H-2L(d)-QL9, the "wild-type" TCR-MHC binding orientation persists despite modified TCR-CDR3alpha interactions with peptide. Thus, a single TCR recognizes two globally similar, but distinct ligands by divergent mechanisms, indicating that receptor-ligand crossreactivity can occur in the absence of molecular mimicry.
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
GLN
ARG62
TYR59
TYR7
GLU163
TRP167
ILE63
MET5
TYR159
TYR171
|
P2
LEU
VAL66
TYR7
GLU163
ILE63
TYR45
TYR159
TYR99
|
P3
SER
GLU114
TYR99
GLN70
TYR159
TYR156
VAL66
ARG97
|
P4
PRO
GLN70
TYR159
TYR155
ARG97
|
P5
PHE
GLY69
TRP73
GLN70
TYR155
|
P6
PRO
GLN70
TYR156
PHE116
TYR155
TRP73
ARG97
|
P7
PHE
ASN77
ALA152
TRP147
TYR155
GLY151
TYR156
ALA150
TRP73
|
P8
ASP
TRP73
LYS146
THR143
ASN77
TRP147
|
P9
LEU
TRP147
THR80
TYR84
PHE116
LEU81
LEU95
TRP73
ILE142
TYR123
LYS146
THR143
ASN77
|
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
VAL66
TYR7
|
B Pocket
SER24
VAL34
TYR45
ILE63
VAL66
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
GPHSMRYFETAVSRRGLGEPRYISVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEYW 70 80 90 100 110 120 ERITQVAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYDG 130 140 150 160 170 180 CDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNGNATLL R |
2. Peptide
|
QLSPFPFDL
|
3. T cell receptor alpha
T cell receptor alpha
TRAV9
|
10 20 30 40 50 60
QSVTQPDARVTVSEGASLQLRCKYSYSATPYLFWYVQYPRQGPQLLLKYYSGDPVVQGVN 70 80 90 100 110 GFEAEFSKSNSSFHLRKASVHRSDSAVYFCAVSHQGRYLTFGSGTKVIVLPYN |
4. T cell receptor beta
T cell receptor beta
TRBV13
|
10 20 30 40 50 60
EAAVTQSPRNKVAVTGEKVTLSCNQTNNHNNMYWYRQDTGHELRLIYYSYGAGSTEKGDI 70 80 90 100 110 120 PDGYKASRPSQENFSLTLESATPSQTSVYFCASGGGGTLYFGAGTRLSVLSSALEHHHHH H |
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.