H2-Kwm7 binding "VNDIFERI" at 2.50Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
H2-Kwm7
VNDIFERI
Species
Locus / Allele group
Predominant occupation of the class I MHC molecule H-2Kwm7 with a single self-peptide suggests a mechanism for its diabetes-protective effect.
Type 1 diabetes (T1D) is an autoimmune disease characterized by T cell-mediated destruction of insulin-producing pancreatic beta cells. In both humans and the non-obese diabetic (NOD) mouse model of T1D, class II MHC alleles are the primary determinant of disease susceptibility. However, class I MHC genes also influence risk. These findings are consistent with the requirement for both CD4(+) and CD8(+) T cells in the pathogenesis of T1D. Although a large body of work has permitted the identification of multiple mechanisms to explain the diabetes-protective effect of particular class II MHC alleles, studies examining the protective influence of class I alleles are lacking. Here, we explored this question by performing biochemical and structural analyses of the murine class I MHC molecule H-2K(wm7), which exerts a diabetes-protective effect in NOD mice. We have found that H-2K(wm7) molecules are predominantly occupied by the single self-peptide VNDIFERI, derived from the ubiquitous protein histone H2B. This unexpected finding suggests that the inability of H-2K(wm7) to support T1D development could be due, at least in part, to the failure of peptides from critical beta-cell antigens to adequately compete for binding and be presented to T cells. Predominant presentation of a single peptide would also be expected to influence T-cell selection, potentially leading to a reduced ability to select a diabetogenic CD8(+) T-cell repertoire. The report that one of the predominant peptides bound by T1D-protective HLA-A*31 is histone derived suggests the potential translation of our findings to human diabetes-protective class I MHC molecules.
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
VAL
TYR171
TYR159
LEU5
TYR59
TYR7
TRP167
GLN63
|
P2
ASN
TYR7
VAL9
ILE66
TYR45
ARG99
GLU24
GLN63
TYR159
ASN70
|
P3
ASP
ILE66
ASN70
ARG99
GLU24
TYR159
|
P4
ILE
ILE66
ARG99
GLY69
ASN70
|
P5
PHE
VAL9
ASN70
ARG99
GLU24
ARG97
TYR22
GLN114
SER73
|
P6
GLU
ARG97
TRP147
ALA150
ASP77
ALA152
ARG155
|
P7
ARG
ARG97
THR143
TRP147
GLN72
SER73
ASP77
VAL76
|
P8
ILE
ARG97
THR143
TYR123
LYS146
TRP147
VAL116
ALA81
ILE95
ASP77
TYR84
THR80
|
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
ALA163
TRP167
TYR171
LEU5
TYR59
GLN63
ILE66
TYR7
|
B Pocket
GLU24
VAL34
TYR45
GLN63
ILE66
ALA67
TYR7
ASN70
VAL9
ARG99
|
C Pocket
ASN70
SER73
SER74
VAL9
ARG97
|
D Pocket
GLN114
ARG155
ASP156
TYR159
LEU160
ARG99
|
E Pocket
GLN114
TRP147
ALA152
ASP156
ARG97
|
F Pocket
VAL116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
ALA81
TYR84
ILE95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD 70 80 90 WSFYILAHTEFTPTETDTYACRVKHDSMAEPKTVYWDRDM |
2. Class I alpha
H2-Kwm7
|
10 20 30 40 50 60
GSHSLRYFVTAVSRPGHGKPRYMEVGYVDDTEFVRFDSDAENPRYEPRTPWMEQVEPEYW 70 80 90 100 110 120 EGQTQIAKGNEQSSRVDLRTALRYYNQSAGGSHTIQRMRGCEVGSDGRLLRGYQQVAYDG 130 140 150 160 170 180 RDYIALNEDLKTWTAADMAALITKHKWEQAGAAERDRAYLEGACVEWLRRYLELGNATLL 190 200 210 220 230 240 RTDSPKAHVTHHSRPKDKVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAGDGT 250 260 270 FQKWASVVVPLGKEQNYTCHVYHEGLPEPLTLRW |
3. Peptide
|
VNDIFERI
|
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.