SLA-1*14:02 binding "DFEREGYSL" at 1.10Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
SLA-1*14:02
DFEREGYSL
Species
Locus / Allele group
Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig.
There is increasing evidence that induction of local immune responses is a key component of effective vaccines. For respiratory pathogens, for example tuberculosis and influenza, aerosol delivery is being actively explored as a method to administer vaccine antigens. Current animal models used to study respiratory pathogens suffer from anatomical disparity with humans. The pig is a natural and important host of influenza viruses and is physiologically more comparable to humans than other animal models in terms of size, respiratory tract biology and volume. It may also be an important vector in the birds to human infection cycle. A major drawback of the current pig model is the inability to analyze antigen-specific CD8+ T-cell responses, which are critical to respiratory immunity. Here we address this knowledge gap using an established in-bred pig model with a high degree of genetic identity between individuals, including the MHC (Swine Leukocyte Antigen (SLA)) locus. We developed a toolset that included long-term in vitro pig T-cell culture and cloning and identification of novel immunodominant influenza-derived T-cell epitopes. We also generated structures of the two SLA class I molecules found in these animals presenting the immunodominant epitopes. These structures allowed definition of the primary anchor points for epitopes in the SLA binding groove and established SLA binding motifs that were used to successfully predict other influenza-derived peptide sequences capable of stimulating T-cells. Peptide-SLA tetramers were constructed and used to track influenza-specific T-cells ex vivo in blood, the lungs and draining lymph nodes. Aerosol immunization with attenuated single cycle influenza viruses (S-FLU) induced large numbers of CD8+ T-cells specific for conserved NP peptides in the respiratory tract. Collectively, these data substantially increase the utility of pigs as an effective model for studying protective local cellular immunity against respiratory pathogens.
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
ASP
TYR60
THR164
ARG63
TYR160
TYR8
SER168
TYR100
ASN64
TYR172
LEU6
|
P2
PHE
TYR100
ASN67
TRP98
ASN64
SER71
SER10
ALA25
MET46
VAL68
TYR160
TYR8
|
P3
GLU
TYR160
HIS156
TYR100
TRP157
TRP98
SER71
ASN67
|
P4
ARG
ASN67
HIS156
TRP157
TRP98
SER71
|
P5
GLU
TRP157
TRP98
PHE117
SER71
ASN75
ASN67
TRP148
ILE74
HIS156
|
P6
GLY
ILE74
HIS156
|
P7
TYR
TRP148
ILE74
ALA151
ASP152
HIS156
ALA153
|
P8
SER
LYS147
TRP148
ILE74
ASN78
|
P9
LEU
ILE143
LYS147
SER144
TRP148
TYR124
LEU96
THR81
ASN78
LEU82
PHE117
TYR85
LEU125
|
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
THR163
SER167
TYR171
LEU5
TYR59
ASN63
ASN66
TYR7
|
B Pocket
ALA24
VAL34
MET45
ASN63
ASN66
VAL67
TYR7
SER70
SER9
TYR99
|
C Pocket
SER70
ILE73
ASN74
SER9
TRP97
|
D Pocket
ASP114
HIS155
TRP156
TYR159
LEU160
TYR99
|
E Pocket
ASP114
TRP147
ALA152
TRP156
TRP97
|
F Pocket
PHE116
TYR123
SER143
LYS146
TRP147
ASN77
THR80
LEU81
TYR84
LEU95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MVARPPKVQVYSRHPAENGKPNYLNCYVSGFHPPQIEIDLLKNGEKMNAEQSDLSFSKDW 70 80 90 SFYLLVHTEFTPNAVDQYSCRVKHVTLDKPKIVKWDRDH |
2. Class I alpha
SLA-1*14:02
IPD-MHC
[ipd-mhc:SLA06136] |
10 20 30 40 50 60
GPHSLSYFSTAVSRPDRGDSRFIAVGYVDDTQFVRFDSDAPNPRMEPRAPWIQQEGQEYW 70 80 90 100 110 120 DRNTRNVMGSAQINRVNLKTLRGYYNQSEAGSHTLQWMYGCYLGPDGLLLRGYDQFAYDG 130 140 150 160 170 180 ADYLALNEDLRSWTAADMAAQISKRKWEAADAAEHWRSYLQGTCVESLRRYLQMGKDTLQ 190 200 210 220 230 240 RAEPPKTHVTRHPSSDLGVTLRCWALGFHPKEISLTWQREGQDQSQDMELVETRPSGDGT 250 260 270 FQKWAALVVPPGEEQSYTCHVQHEGLQEPLTLRWD |
3. Peptide
|
DFEREGYSL
|
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.