Rano-A*av1 binding "YLRYDSDVGEYR" at 2.90Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Rano-A*av1
YLRYDSDVGEYR
Species
Locus / Allele group
Cross-Reactive Donor-Specific CD8+ Tregs Efficiently Prevent Transplant Rejection.
To reduce the use of non-specific immunosuppressive drugs detrimental to transplant patient health, therapies in development aim to achieve antigen-specific tolerance by promoting antigen-specific regulatory T cells (Tregs). However, identification of the natural antigens recognized by Tregs and the contribution of their dominance in transplantation has been challenging. We identify epitopes derived from distinct major histocompatibility complex (MHC) class II molecules, sharing a 7-amino acid consensus sequence positioned in a central mobile section in complex with MHC class I, recognized by cross-reactive CD8+ Tregs, enriched in the graft. Antigen-specific CD8+ Tregs can be induced in vivo with a 16-amino acid-long peptide to trigger transplant tolerance. Peptides derived from human HLA class II molecules, harboring the rat consensus sequence, also activate and expand human CD8+ Tregs, suggesting its potential in human transplantation. Altogether, this work should facilitate the development of therapies with peptide epitopes for transplantation and improve our understanding of CD8+ Treg recognition.
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
TRP167
LEU5
TYR171
TYR99
TYR7
TYR159
THR163
TYR59
GLN63
ILE66
GLN62
|
P10
GLU
TRP70
ILE73
TYR152
ASP77
TRP147
|
P11
TYR
ASP77
TRP147
VAL76
GLN72
ILE73
LYS146
|
P12
ARG
TYR74
TRP147
LEU81
THR80
GLN96
ASP77
ASP116
ARG114
TYR84
GLU97
TYR123
ILE95
LYS146
THR143
|
P2
LEU
MET45
TYR159
GLN63
ILE66
ALA67
TYR9
TYR7
TYR99
|
P3
ARG
TYR9
TYR152
TYR99
ARG114
TYR159
ILE66
TRP70
GLU97
LEU156
|
P4
TYR
TYR159
GLU69
ILE66
TRP70
|
P5
ASP
ARG155
|
P6
SER
GLU69
ILE73
|
P8
VAL
ARG155
TYR152
ALA150
|
P9
GLY
ILE73
|
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
GLN63
ILE66
TYR7
|
B Pocket
ALA24
VAL34
MET45
GLN63
ILE66
ALA67
TYR7
TRP70
TYR9
TYR99
|
C Pocket
TRP70
ILE73
TYR74
TYR9
GLU97
|
D Pocket
ARG114
ARG155
LEU156
TYR159
LEU160
TYR99
|
E Pocket
ARG114
TRP147
TYR152
LEU156
GLU97
|
F Pocket
ASP116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
LEU81
TYR84
ILE95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MIQKTPQIQVYSRHPPENGKPNFLNCYVSQFHPPQIEIELLKNGKKIPNIEMSDLSFSKD 70 80 90 WSFYILAHTEFTPTETDVYACRVKHVTLKEPKTVTWDRDM |
2. Class I alpha
Rano-A*av1
IPD-MHC
[ipd-mhc:RT108344] |
10 20 30 40 50 60
GSHSLRYFYTAVSRPGLGEPRFIAVGYVDDTEFVRFDSDAENPRMEPRARWMEREGPEYW 70 80 90 100 110 120 EQQTRIAKEWEQIYRVDLRTLRGYYNQSEGGSHTIQEMYGCDVGSDGSLLRGYRQDAYDG 130 140 150 160 170 180 RDYIALNEDLKTWTAADFAAQITRNKWERARYAERLRAYLEGTCVEWLSRYLELGKETLL 190 200 210 220 230 240 RSDPPEAHVTLHPRPEGDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGT 250 260 270 FQKWASVVVPLGKEQNYTCRVEHEGLPKPLSQRWE |
3. Peptide
|
YLRYDSDVGEYR
|
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
Complete structures
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.