DLA-88*50801: binding "RFLDKDGFIDK" at 2.00Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
DLA-88*50801:
RFLDKDGFIDK
Species
Locus / Allele group
Diversified Anchoring Features the Peptide Presentation of DLA-88*50801: First Structural Insight into Domestic Dog MHC Class I.
Canines represent a crucial animal model for studying human diseases and organ transplantation, as well as the evolution of domestic animals. MHCs, with a central role in cellular immunity, are commonly used in the study of dog population genetics and genome evolution. However, the molecular basis for the peptide presentation of dog MHC remains largely unknown. In this study, peptide presentation by canine MHC class I DLA-88*50801 was structurally determined, revealing diversified anchoring modes of the binding peptides. Flexible and large pockets composed of both hydrophobic and hydrophilic residues can accommodate pathogen-derived peptides with diverse anchor residues, as confirmed by thermostability measurements. Furthermore, DLA-88*50801 contains an unusual α2 helix with a large coil in the TCR contact region. These results further our understanding of canine T cell immunity through peptide presentation of MHC class I and shed light on the molecular basis for vaccine development for canine infectious diseases, for example, canine distemper virus.
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
ARG
TYR59
LYS66
GLU63
GLU58
TYR99
TYR160
GLY62
TYR172
LEU5
TRP168
TYR7
|
P10
ASP
LYS146
TRP147
VAL73
THR143
VAL76
ASP77
|
P11
LYS
THR97
ILE95
TYR74
THR143
TYR123
ASP77
ILE124
THR80
ASP116
LEU81
LYS146
TRP147
ILE142
ARG114
TYR84
|
P2
PHE
VAL34
TYR7
LYS66
GLU63
TYR99
TYR160
THR45
ALA24
VAL67
TYR9
|
P3
LEU
TYR9
THR70
TYR99
LYS66
TYR160
GLN156
TRP157
|
P4
ASP
GLN156
LYS66
THR70
|
P5
LYS
GLU69
THR70
LYS66
VAL73
|
P6
ASP
VAL152
GLN156
|
P7
GLY
VAL152
ARG114
GLN156
TRP157
|
P8
PHE
VAL152
THR70
TYR99
ARG114
THR97
TRP157
TYR9
VAL73
TYR74
|
P9
ILE
ASP77
VAL152
LYS146
TRP147
ALA150
VAL73
|
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]
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MAPRPALATAGFLALLLILLAACRLDAVQHPPKIQVYSRHPAENGKPNFLNCYVSGFHPP 70 80 90 100 110 120 EIEIDLLKNGKEMKAEQTDLSFSKDWTFYLLVHTEFTPNEQDEFSCRVKHVTLSEPQIVK WDRDN |
2. Class I alpha
DLA-88*50801:
|
10 20 30 40 50 60
GSHSLRYFYTSVSRPGRGDPRFIAVGYVDDTQFVRFDSDAATGRTEPRAPWVEQEGPEYW 70 80 90 100 110 120 DGETRKVKETAQVYRVDLDTLRGYYNQSEAGSHTIQTMYGCDLGPGGRLLRGYRQDAYDG 130 140 150 160 170 180 ADYIALNEDLRSWTAADTAAQITRRKWEAAGVAELQWRNYLETTCVEWLQRYLEMGKETL 190 200 210 220 230 240 LRAEPPSTRVTRHPISDHEVTLRCWALGFYPAEITLTWQRDGEDQTQDTEVVDTRPAGDG 250 260 270 TFQKWAAVVVPSGQEQRYTCHVQHEGLVEPVTRRW |
3. Peptide
|
RFLDKDGFIDK
|
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.