BoLA-N*13:01 binding "VGYPKVKEEML" at 1.90Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
BoLA-N*13:01
VGYPKVKEEML
Species
Locus / Allele group
MHC class I bound to an immunodominant Theileria parva epitope demonstrates unconventional presentation to T cell receptors.
T cell receptor (TCR) recognition of peptide-MHC class I (pMHC) complexes is a crucial event in the adaptive immune response to pathogens. Peptide epitopes often display a strong dominance hierarchy, resulting in focusing of the response on a limited number of the most dominant epitopes. Such T cell responses may be additionally restricted by particular MHC alleles in preference to others. We have studied this poorly understood phenomenon using Theileria parva, a protozoan parasite that causes an often fatal lymphoproliferative disease in cattle. Despite its antigenic complexity, CD8+ T cell responses induced by infection with the parasite show profound immunodominance, as exemplified by the Tp1(214-224) epitope presented by the common and functionally important MHC class I allele N*01301. We present a high-resolution crystal structure of this pMHC complex, demonstrating that the peptide is presented in a distinctive raised conformation. Functional studies using CD8+ T cell clones show that this impacts significantly on TCR recognition. The unconventional structure is generated by a hydrophobic ridge within the MHC peptide binding groove, found in a set of cattle MHC alleles. Extremely rare in all other species, this feature is seen in a small group of mouse MHC class I molecules. The data generated in this analysis contribute to our understanding of the structural basis for T cell-dependent immune responses, providing insight into what determines a highly immunogenic p-MHC complex, and hence can be of value in prediction of antigenic epitopes and vaccine design.
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
P10
TYR
TYR99
ASN70
TYR159
ILE66
ALA152
PHE156
ARG155
|
P11
PRO
ARG155
ASN70
ARG62
ILE66
|
P12
LYS
HIS9
GLU114
ARG155
GLU97
GLU69
TRP73
TYR74
TYR116
ASN70
|
P13
VAL
ARG155
TRP73
|
P14
LYS
LEU72
GLU76
GLU69
TRP73
|
P15
GLU
ALA150
|
P16
GLU
MET147
GLY151
ARG155
ALA150
TRP73
ALA152
|
P17
MET
LYS146
SER143
GLU76
TRP73
ASN80
MET147
ALA77
|
P18
LEU
MET147
LEU95
TYR123
LYS146
TYR84
TRP73
TYR116
LEU81
SER143
LEU124
ILE142
ALA77
ASN80
|
P8
VAL
LEU5
TRP167
TYR159
TYR59
TYR7
ARG62
THR163
GLU63
TYR171
|
P9
GLY
TYR99
ARG62
TYR159
TYR7
ILE66
GLU63
|
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
TRP167
TYR171
LEU5
TYR59
GLU63
ILE66
TYR7
|
B Pocket
THR24
VAL34
THR45
GLU63
ILE66
SER67
TYR7
ASN70
HIS9
TYR99
|
C Pocket
ASN70
TRP73
TYR74
HIS9
GLU97
|
D Pocket
GLU114
ARG155
PHE156
TYR159
LEU160
TYR99
|
E Pocket
GLU114
MET147
ALA152
PHE156
GLU97
|
F Pocket
TYR116
TYR123
SER143
LYS146
MET147
ALA77
ASN80
LEU81
TYR84
LEU95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
AIQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDW 70 80 90 SFYLLSHAEFTPNSKDQYSCRVKHVTLEQPRIVKWDRDL |
2. Class I alpha
BoLA-N*13:01
|
10 20 30 40 50 60
GSHSLRYFHTAVSRPGLREPLFITVGYVDDTQFVRFDSDARDPRTEPRQPWMEKEGPEYW 70 80 90 100 110 120 DRETQISKENALWYREALNNLRGYYNQSEAGSHTLQEMYGCDVGSDGRLRRGYEQYGYDG 130 140 150 160 170 180 RDYLALNEDLRSWTAADTAAQISKRKMEAAGAAERFRNYLEGTCVEWLRRYLENGKDTLL 190 200 210 220 230 240 RADPPKAHVTRHPSSEHEVTLRCWALGFYPEEISLTWQRNGEDQTQDMELVETRPSGDGN 250 260 270 FQKWAALVVPSGEEQRYTCRVQHEGLQEPLTLRWEPG |
3. Peptide
|
VGYPKVKEEML
|
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.