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5WJN

HLA-A*11:01 binding "GTSGSPIINR" at 2.85Å resolution

Data provenance

Structure downloaded from PDB Europe using the Coordinate Server. Aligned to residues 1-180 of 1HHK2 using the CEALIGN3 function of PyMol4. Chain assigment using a Levenshtein distance5 method using data from the PDBe REST API6. Organism data from PDBe REST API. Data for both of these operations from the Molecules endpoint. Structure visualised with 3DMol7.

Information sections


Complex type

Class i with peptide

1. Beta 2 microglobulin
['B', 'E', 'H']
2. Class I alpha
HLA-A*11:01
['A', 'D', 'G']
3. Peptide
GTSGSPIINR
['C', 'F', 'I']

Species


Locus / Allele group


Publication

Germline bias dictates cross-serotype reactivity in a common dengue-virus-specific CD8(+) T cell response.

Culshaw A, Ladell K, Gras S, McLaren JE, Miners KL, Farenc C, van den Heuvel H, Gostick E, Dejnirattisai W, Wangteeraprasert A, Duangchinda T, Chotiyarnwong P, Limpitikul W, Vasanawathana S, Malasit P, Dong T, Rossjohn J, Mongkolsapaya J, Price DA, Screaton GR
Nat. Immunol. (2017) [doi:10.1038/ni.3850]  [pubmed:28945243

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

Deposited: 2017-07-23
Released: 2017-09-20
Revised: 2017-10-25

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Decamer (10 amino acids)

Sequence: GTSGSPIINR

Interactive view
Cutaway side view (static)
Surface top view (static - coloured by atom property)
Cutaway top view (static)

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
TRP167
MET5
GLU63
TYR171
PHE33
TYR159
TYR7
P10 ARG

ILE142
LYS146
THR143
ILE97
ASP74
TRP147
TYR123
LEU81
ILE95
THR80
ASP116
GLN70
THR73
ASP77
ARG114
TYR84
P2 THR

TYR159
TYR9
ARG163
ASN66
TYR7
MET45
TRP167
VAL67
TYR99
GLU63
P3 SER

GLN156
TYR159
TYR9
ASN66
TYR99
P4 GLY

ARG163
ASN66
P5 SER

GLN155
P6 PRO

ALA152
GLN156
GLN155
P7 ILE

THR73
ASN66
GLN70
ALA69
P8 ILE

TRP147
GLN155
ALA150
ALA152
THR73
ASP77
P9 ASN

THR73
ASP77
LYS146
TRP147
VAL76

Colour key

Aromatic Hydrophobic Acidic Basic Neutral/polar

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]


Binding cleft pockets


Peptide sidechain binding pockets (static)
Peptide terminii and backbone binding residues (static)
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

Binds N-terminus Binds P1 backbone Binds P2 backbone Binds PC-1 backbone Binds C-terminus

Data provenance

N-/C-terminus and peptide backbone binding residues are assigned according to previously published information and pockets are assigned according to an adaptation of a previously published set of residues. All numbering is currently that of the 'canonical' structures of human and mouse MHC Class I molecules.

Chain sequences

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
GTSGSPIINR


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

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Please take note of the data license. Using data from this site assumes that you have read and will comply with the license.

Complete structures

Aligned structures [cif]
  1. 5WJN assembly 1  
  2. 5WJN assembly 2  
  3. 5WJN assembly 3  

Components

MHC Class I alpha chain [cif]
  1. 5WJN assembly 1  
  2. 5WJN assembly 2  
  3. 5WJN assembly 3  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5WJN assembly 1  
  2. 5WJN assembly 2  
  3. 5WJN assembly 3  
Peptide only [cif]
  1. 5WJN assembly 1  
  2. 5WJN assembly 2  
  3. 5WJN assembly 3  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5wjn

Data license

The data above is made available under a Creative Commons CC-BY 4.0 license. This means you can copy, remix, transform, build upon and redistribute the material, but you must give appropriate credit, provide a link to the license, and indicate if changes were made.
If you use any data downloaded from this site in a publication, please cite 'https://www.histo.fyi/'. A preprint is in preparation.

Footnotes