H2-Kd binding "YQSGLSIVM" at 2.25Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
H2-Kd
YQSGLSIVM
Species
Locus / Allele group
MHC-restricted Ag85B-specific CD8+ T��cells are enhanced by recombinant BCG prime and DNA boost immunization in mice.
Despite efforts to develop effective treatments and vaccines, Mycobacterium tuberculosis (Mtb), particularly pulmonary Mtb, continues to provide major health challenges worldwide. To improve immunization against the persistent health challenge of Mtb infection, we have studied the CD8+ T cell response to Bacillus Calmette-Guérin (BCG) and recombinant BCG (rBCG) in mice. Here, we generated CD8+ T cells with an rBCG-based vaccine encoding the Ag85B protein of M. kansasii, termed rBCG-Mkan85B, followed by boosting with plasmid DNA expressing the Ag85B gene (DNA-Mkan85B). We identified two MHC-I (H2-Kd )-restricted epitopes that induce cross-reactive responses to Mtb and other related mycobacteria in both BALB/c (H2d ) and CB6F1 (H2b/d ) mice. The H2-Kd -restricted peptide epitopes elicited polyfunctional CD8+ T cell responses that were also highly cross-reactive with those of other proteins of the Ag85 complex. Tetramer staining indicated that the two H2-Kd -restricted epitopes elicit distinct CD8+ T cell populations, a result explained by the X-ray structure of the two peptide/H2-Kd complexes. These results suggest that rBCG-Mkan85B vector-based immunization and DNA-Mkan85B boost may enhance CD8+ T cell response to Mtb, and might help to overcome the limited effectiveness of the current BCG in eliciting tuberculosis immunity.
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
TYR
PHE22
PHE74
ASP70
TYR159
TYR7
ARG66
PHE99
VAL9
GLN63
ALA67
PHE45
ALA24
ARG97
|
P2
GLN
TYR156
TYR155
PHE99
ARG97
ASP70
TYR159
ARG66
|
P3
SER
GLN65
ARG66
SER69
ALA67
TYR156
TYR155
ARG97
ASP70
|
P4
GLY
TYR156
TYR155
TRP73
ARG97
ASP70
|
P5
LEU
TYR156
TYR155
TRP73
ASP152
|
P6
SER
TRP73
TRP147
ASP152
ALA150
LYS146
TYR156
|
P7
ILE
SER77
LYS146
TRP73
VAL76
THR80
TRP147
|
P8
VAL
LYS146
ALA81
PHE95
TRP73
SER77
THR80
TRP147
ILE142
THR143
TYR123
|
P9
MET
ALA139
LYS146
TYR123
THR80
ILE142
THR143
TYR84
|
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
LEU159
CYS163
LEU167
LEU171
ARG5
TRP59
THR63
ALA66
PHE7
|
B Pocket
VAL24
ARG34
GLU45
THR63
ALA66
LYS67
PHE7
GLU70
THR9
GLY99
|
C Pocket
GLU70
PHE73
ARG74
THR9
MET97
|
D Pocket
GLN114
TYR155
ARG156
LEU159
GLU160
GLY99
|
E Pocket
GLN114
GLU147
ALA152
ARG156
MET97
|
F Pocket
ALA116
ILE123
ARG143
TRP146
GLU147
LEU77
ALA80
GLN81
TYR84
GLN95
|
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-Kd
|
10 20 30 40 50 60
PHSLRYFVTAVSRPGLGEPRFIAVGYVDDTQFVRFDSDADNPRFEPRAPWMEQEGPEYWE 70 80 90 100 110 120 EQTQRAKSDEQWFRVSLRTAQRYYNQSKGGSHTFQRMFGCDVGSDWRLLRGYHQFAYDGR 130 140 150 160 170 180 DYIALNEDLKTWTAADTAALITRRKWEQAGDAEYYRAYLEGECVEWLRRYLELGNETLLR 190 200 210 220 230 240 TDSPKAHVTYHPRSQVDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGTF 250 260 270 QKWAAVVVPLGKEQNYTCHVHHKGLPEPLTLRWKP |
3. Peptide
|
YQSGLSIVM
|
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.