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5WMQ

HLA-B*08:01 binding "ELRSRYWAI" at 1.40Å 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']
2. Class I alpha
HLA-B*08:01
['A']
3. Peptide
ELRSRYWAI
['C']

Species


Locus / Allele group


Publication

Inability To Detect Cross-Reactive Memory T Cells Challenges the Frequency of Heterologous Immunity among Common Viruses.

Rowntree LC, Nguyen THO, Halim H, Purcell AW, Rossjohn J, Gras S, Kotsimbos TC, Mifsud NA
J. Immunol. (2018) [doi:10.4049/jimmunol.1800010]  [pubmed:29735483

Human memory T cells that cross-react with epitopes from unrelated viruses can potentially modulate immune responses to subsequent infections by a phenomenon termed heterologous immunity. However, it is unclear whether similarities in structure rather than sequence underpin heterologous T cell cross-reactivity. In this study, we aimed to explore the mechanism of heterologous immunity involving immunodominant epitopes derived from common viruses restricted to high-frequency HLA allotypes (HLA-A*02:01, -B*07:02, and -B*08:01). We examined EBV-specific memory T cells for their ability to cross-react with CMV or influenza A virus-derived epitopes. Following T cell immunoassays to determine phenotype and function, complemented with biophysical and structural investigations of peptide/HLA complexes, we did not detect cross-reactivity of EBV-specific memory T cells toward either CMV or influenza A virus epitopes presented by any of the selected HLA allomorphs. Thus, despite the ubiquitous nature of these human viruses and the dominant immune response directed toward the selected epitopes, heterologous virus-specific T cell cross-reactivity was not detected. This suggests that either heterologous immunity is not as common as previously reported, or that it requires a very specific biological context to develop and be clinically relevant.

Structure deposition and release

Deposited: 2017-07-31
Released: 2018-06-06
Revised: 2020-02-26

Data provenance

Publication data retrieved from PDBe REST API8 and PMCe REST API9

Other structures from this publication


Peptide details

Length: Nonamer (9 amino acids)

Sequence: ELRSRYWAI

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 GLU

ARG62
TYR59
TYR7
ILE66
THR163
ASN63
TRP167
PHE33
MET5
TYR171
TYR159
P2 LEU

ILE66
PHE67
TYR159
TYR99
TYR7
ASN70
SER24
ASN63
PHE36
P3 ARG

ASN70
ASP156
ASN114
ILE66
TYR116
TYR159
TYR99
P4 SER

ILE66
ASN70
P5 ARG

THR69
ASN70
ASP74
SER97
TYR116
THR73
TYR99
ASP9
P6 TYR

THR73
THR69
P7 TRP

THR73
GLN155
ALA150
VAL152
TRP147
P8 ALA

THR73
GLU76
SER77
ASN80
THR143
LYS146
TRP147
P9 ILE

LYS146
TYR116
TRP147
ILE124
LEU81
ASN80
TYR84
LEU95
GLU76
SER77
THR143
TYR123

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
THR163
TRP167
TYR171
MET5
TYR59
ASN63
ILE66
TYR7
B Pocket

SER24
VAL34
MET45
ASN63
ILE66
PHE67
TYR7
ASN70
ASP9
TYR99
C Pocket

ASN70
THR73
ASP74
ASP9
SER97
D Pocket

ASN114
GLN155
ASP156
TYR159
LEU160
TYR99
E Pocket

ASN114
TRP147
VAL152
ASP156
SER97
F Pocket

TYR116
TYR123
THR143
LYS146
TRP147
SER77
ASN80
LEU81
TYR84
LEU95

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-B*08:01
IPD-IMGT/HLA
[ipd-imgt:HLA34671]
        10        20        30        40        50        60
GSHSMRYFDTAMSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRMEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DRNTQIFKTNTQTDRESLRNLRGYYNQSEAGSHTLQSMYGCDVGPDGRLLRGHNQYAYDG
       130       140       150       160       170       180
KDYIALNEDLRSWTAADTAAQITQRKWEAARVAEQDRAYLEGTCVEWLRRYLENGKDTLE
       190       200       210       220       230       240
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
       250       260       270
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

3. Peptide
ELRSRYWAI


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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Complete structures

Aligned structures [cif]
  1. 5WMQ assembly 1  

Components

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

Derived data

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

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