H2-Dd binding "RGPGRAFVTI" with Ly49a NK receptor at 2.30Å resolution
Data provenance
Information sections
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
Class i with peptide and ly49a
H2-Dd
RGPGRAFVTI
Species
Locus / Allele group
Crystal structure of a lectin-like natural killer cell receptor bound to its MHC class I ligand.
The neuroactive mycotoxin lolitrem B causes a neurological syndrome in grazing livestock resulting in hyperexcitability, muscle tremors, ataxia and, in severe cases, clonic seizures and death. To define the effects of the major toxin lolitrem B in the brain, a functional metabolomic study was undertaken in which motor coordination and tremor were quantified and metabolomic profiling undertaken to determine relative abundance of both toxin and key neurotransmitters in various brain regions in male mice. Marked differences were observed in the duration of tremor and coordination between lolitrem B pathway members, with some showing protracted effects and others none at all. Lolitrem B was identified in liver, kidney, cerebral cortex and thalamus but not in brainstem or cerebellum which were hypothesised previously to be the primary site of action. Metabolomic profiling showed significant variation in specific neurotransmitter and amino acid profiles over time. This study demonstrates accumulation of lolitrem B in the brain, with non-detectable levels of toxin in the brainstem and cerebellum, inducing alterations in metabolites such as tyrosine, suggesting a dynamic catecholaminergic response over time. Temporal characterisation of key pathways in the pathophysiological response of lolitrem B in the brain were also identified.
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
GLU163
LEU5
ARG62
TRP167
TYR7
TYR159
TYR59
ARG66
GLU58
TYR171
GLU63
|
P10
ILE
TYR123
TRP147
THR143
TYR84
ALA81
ILE142
LYS146
ASP77
THR80
|
P2
GLY
GLU63
GLU163
TYR7
TYR159
ARG66
|
P3
PRO
TYR7
ASN70
TRP97
TYR159
ARG66
ALA99
TRP114
|
P4
GLY
ARG66
TRP97
TRP114
ASN70
|
P5
ARG
ASN70
PHE74
SER73
TRP147
TRP97
PHE116
TRP114
ARG155
ASP77
|
P6
ALA
ARG155
ASN70
SER73
|
P7
PHE
GLN72
GLY69
SER73
|
P8
VAL
ALA152
ARG155
SER73
TRP147
|
P9
THR
TRP147
LYS146
ASP77
SER73
VAL76
THR143
|
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
GLU163
TRP167
TYR171
LEU5
TYR59
GLU63
ARG66
TYR7
|
B Pocket
GLU24
VAL34
TYR45
GLU63
ARG66
ALA67
TYR7
ASN70
VAL9
ALA99
|
C Pocket
ASN70
SER73
PHE74
VAL9
TRP97
|
D Pocket
TRP114
ARG155
ASP156
TYR159
LEU160
ALA99
|
E Pocket
TRP114
TRP147
ALA152
ASP156
TRP97
|
F Pocket
PHE116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
ALA81
TYR84
LEU95
|
Colour key
Data provenance
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD 70 80 90 WSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM |
2. Class I alpha
H2-Dd
|
10 20 30 40 50 60
MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYW 70 80 90 100 110 120 ERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDG 130 140 150 160 170 180 CDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLL 190 200 210 220 230 240 RTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGT 250 260 270 FQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGKE |
3. Natural Killer Cell Receptor Ly49a
Natural Killer Cell Receptor Ly49a
|
10 20 30 40 50 60
STVLDSLQHTGRGDKVYWFCYGMKCYYFVMDRKTWSGCKQTCQSSSLSLLKIDDEDELKF 70 80 90 100 110 120 LQLVVPSDSCWVGLSYDNKKKDWAWIDNRPSKLALNTRKYNIRDGGCMLLSKTRLDNGNC 130 DQVFICICGKRLDKFPH |
4. Peptide
|
RGPGRAFVTI
|
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.