HLA-A*11:01 presenting "GTSGSPIVNR" to Alpha/Beta T cell receptor at 2.95Å 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 alpha beta tcr
HLA-A*11:01
GTSGSPIVNR
TRAV30
TRBV11
Species
Locus / Allele group
Germline bias dictates cross-serotype reactivity in a common dengue-virus-specific CD8(+) T cell response.
Traumatic brain injury (TBI) leads to a deleterious neuroinflammation, originating from microglial activation. Monitoring microglial activation is an indispensable step to develop therapeutic strategies for TBI. In this study, we evaluated the use of the 18-kDa translocator protein (TSPO) in positron emission tomography (PET) and cellular analysis to monitor microglial activation in a mild TBI mouse model. TBI was induced on male Swiss mice. PET imaging analysis with [18F]FEPPA, a TSPO radiotracer, was performed at 1, 3 and 7 days post-TBI and flow cytometry analysis on brain at 1 and 3 days post-TBI. PET analysis showed no difference in TSPO expression between non-operated, sham-operated and TBI mice. Flow cytometry analysis demonstrated an increase in TSPO expression in ipsilateral brain 3 days post-TBI, especially in microglia, macrophages, lymphocytes and neutrophils. Moreover, microglia represent only 58.3% of TSPO+ cells in the brain. Our results raise the question of the use of TSPO radiotracer to monitor microglial activation after TBI. More broadly, flow cytometry results point the lack of specificity of TSPO for microglia and imply that microglia contribute to the overall increase in TSPO in the brain after TBI, but is not its only contributor.
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
GLY
TYR59
TYR7
MET5
TRP167
PHE33
TYR171
TYR159
GLU63
|
P10
ARG
LEU81
ILE95
ILE142
ASP77
THR73
ARG114
ASP74
TYR84
THR143
TYR123
ILE124
TRP147
THR80
ASP116
GLN70
ILE97
LYS146
|
P2
THR
TYR99
MET45
TYR9
TYR159
TYR7
GLU63
ASN66
GLN62
VAL67
|
P3
SER
TYR9
TYR159
TYR99
ASN66
GLN156
|
P4
GLY
ASN66
|
P5
SER
TYR159
GLN155
GLN156
|
P6
PRO
GLN155
ARG114
GLN156
ALA152
GLN70
|
P7
ILE
GLN70
ASN66
THR73
ALA69
|
P8
VAL
ASP77
ALA150
THR73
TRP147
ALA152
|
P9
ASN
TRP147
LYS146
VAL76
ASP77
THR73
|
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
ARG163
TRP167
TYR171
MET5
TYR59
GLU63
ASN66
TYR7
|
B Pocket
ALA24
VAL34
MET45
GLU63
ASN66
VAL67
TYR7
GLN70
TYR9
TYR99
|
C Pocket
GLN70
THR73
ASP74
TYR9
ILE97
|
D Pocket
ARG114
GLN155
GLN156
TYR159
LEU160
TYR99
|
E Pocket
ARG114
TRP147
ALA152
GLN156
ILE97
|
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
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD 70 80 90 WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM |
2. Class I alpha
HLA-A*11:01
IPD-IMGT/HLA
[ipd-imgt:HLA34732] |
10 20 30 40 50 60
GSHSMRYFYTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW 70 80 90 100 110 120 DQETRNVKAQSQTDRVDLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDG 130 140 150 160 170 180 KDYIALNEDLRSWTAADMAAQITKRKWEAAHAAEQQRAYLEGRCVEWLRRYLENGKETLQ 190 200 210 220 230 240 RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT 250 260 270 FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW |
3. Peptide
|
GTSGSPIVNR
|
4. T cell receptor alpha
T cell receptor alpha
TRAV30
|
10 20 30 40 50 60
QPVQSPQAVILREGEDAIINCSSSKALYSVHWYRQKHGEAPIFLMILLKGGEQKGHDKIS 70 80 90 100 110 120 ASFNEKKQQSSLYLTASQLSYSGTYFCGLGDAGNMLTFGGGTRLMVKPHIQNPDPAVYQL 130 140 150 160 170 180 RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFA 190 CANAFNNSIIPEDTFFPS |
5. T cell receptor beta
T cell receptor beta
TRBV11
|
10 20 30 40 50 60
AGVAQSPRYKIIEKRQSVAFWCNPISGHATLYWYQQILGQGPKLLIQFQNNGVVDDSQLP 70 80 90 100 110 120 KDRFSAERLKGVDSTLKIQPAKLEDSAVYLCASSLGQGLLYGYTFGSGTRLTVLEDLNKV 130 140 150 160 170 180 FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ 190 200 210 220 230 240 PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW GRAD |
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.