H2-Db presenting "SSLCNFRAYV" to Alpha/Beta T cell receptor at 1.87Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Class i with peptide and alpha beta tcr
H2-Db
SSLCNFRAYV
TRAV21
TRBV29
Species
Locus / Allele group
Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus.
Interactions between a T cell receptor (TCR) and a peptide-major histocompatibility complex (pMHC) ligand are typically mediated by noncovalent bonds. By studying T cells expressing natural or engineered TCRs, here we describe covalent TCR-pMHC interactions that involve a cysteine-cysteine disulfide bond between the TCR and the peptide. By introducing cysteines into a known TCR-pMHC combination, we demonstrate that disulfide bond formation does not require structural rearrangement of the TCR or the peptide. We further show these disulfide bonds still form even when the initial affinity of the TCR-pMHC interaction is low. Accordingly, TCR-peptide disulfide bonds facilitate T cell activation by pMHC ligands with a wide spectrum of affinities for the TCR. Physiologically, this mechanism induces strong Zap70-dependent TCR signaling, which triggers T cell deletion or agonist selection in the thymus cortex. Covalent TCR-pMHC interactions may thus underlie a physiological T cell activation mechanism that has applications in basic immunology and potentially in immunotherapy.
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
PHE33
TYR171
MET5
TYR7
GLU163
TYR159
TYR59
GLU63
TRP167
LYS66
|
P10
VAL
TRP147
TYR84
TYR123
LEU95
LYS146
THR143
ASN80
LEU81
SER77
TRP73
|
P2
SER
TYR45
TYR159
LYS66
TYR7
GLU63
GLU163
|
P3
LEU
GLU9
GLN70
SER99
TYR7
LEU114
TYR159
LYS66
GLN97
TYR156
HIS155
|
P4
CYS
LYS66
TYR156
HIS155
GLN70
|
P5
ASN
GLN70
TRP73
TYR156
GLU9
PHE74
GLN97
PHE116
HIS155
|
P6
PHE
TYR156
HIS155
SER150
ALA152
TRP73
GLY151
|
P7
ARG
TRP73
|
P8
ALA
TRP147
LYS146
TYR156
TRP73
SER150
|
P9
TYR
TRP73
TRP147
LYS146
THR143
GLN72
VAL76
SER77
ASN80
|
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
GLU63
LYS66
TYR7
|
B Pocket
SER24
VAL34
TYR45
GLU63
LYS66
ALA67
TYR7
GLN70
GLU9
SER99
|
C Pocket
GLN70
TRP73
PHE74
GLU9
GLN97
|
D Pocket
LEU114
HIS155
TYR156
TYR159
LEU160
SER99
|
E Pocket
LEU114
TRP147
ALA152
TYR156
GLN97
|
F Pocket
PHE116
TYR123
THR143
LYS146
TRP147
SER77
ASN80
LEU81
TYR84
LEU95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD 70 80 90 WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM |
2. Class I alpha
H2-Db
|
10 20 30 40 50 60
GPHSMRYFETAVSRPGLEEPRYISVGYVDNKEFVRFDSDAENPRYEPRAPWMEQEGPEYW 70 80 90 100 110 120 ERETQKAKGQEQWFRVSLRNLLGYYNQSAGGSHTLQQMSGCDLGSDWRLLRGYLQFAYEG 130 140 150 160 170 180 RDYIALNEDLKTWTAADMAAQITRRKWEQSGAAEHYKAYLEGECVEWLHRYLKNGNATLL 190 200 210 220 230 240 RTDSPKAHVTHHPRSKGEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT 250 260 270 FQKWASVVVPLGKEQNYTCRVYHEGLPEPLTLRWEPS |
3. Peptide
|
SSLCNFRAYV
|
4. T cell receptor alpha
T cell receptor alpha
TRAV21
|
10 20 30 40 50 60
DAKTTQPDSMESTEGETVHLPCSHATISGNEYIYWYRQVPLQGPEYVTHGLQQNTTNSMA 70 80 90 100 110 120 FLAIASDRKSSTLILPHVSLRDAAVYHCILSGGCNYKLTFGKGTLLTVTPNIQNPDPAVY 130 140 150 160 170 180 QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD 190 200 FACANAFNNSIIPEDTFFPSPESS |
5. T cell receptor beta
T cell receptor beta
TRBV29
|
10 20 30 40 50 60
DMKVTQMPRYLIKRMGENVLLECGQDMSHETMYWYRQDPGLGLQLIYISYDVDSNSEGDI 70 80 90 100 110 120 PKGYRVSRKKREHFSLILDSAKTNQTSVYFCASSFGREQYFGPGTRLTVLEDLKNVFPPE 130 140 150 160 170 180 VAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALN 190 200 210 220 230 DSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD |
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.