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7PBE

HLA-A*02:01 presenting "YLQPRTFLL" to Alpha/Beta T cell receptor at 3.00Å 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 and alpha beta tcr

1. Beta 2 microglobulin
['B', 'G']
2. Class I alpha
HLA-A*02:01
['A', 'F']
3. Peptide
YLQPRTFLL
['C', 'H']
4. T cell receptor alpha
TRAV12
['D']
5. T cell receptor beta
TRBV7
['E']

Species


Locus / Allele group


Publication

Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope.

Dolton G, Rius C, Hasan MS, Wall A, Szomolay B, Behiry E, Whalley T, Southgate J, Fuller A, Morin T, Topley K, Tan LR, Goulder PJR, Spiller OB, Rizkallah PJ, Jones LC, Connor TR, Sewell AK
Cell (2022) 185, 2936-2951.e19 [doi:10.1016/j.cell.2022.07.002]  [pubmed:35931021

Since the onset of the pandemic, multiple SARS-CoV-2 variants have emerged with increasing ability to evade neutralizing antibodies. Thus, earlier interest in defining the correlates of protection from infection, mainly mediated by humoral immunity, has shifted to correlates of protection from disease, which require a more comprehensive analysis of both humoral and cellular immunity. In this review, we summarized the evidence that supports the role of SARS-CoV-2-specific T cells induced by infection, by vaccination or by their combination (defined as hybrid immunity) in disease protection. We then analyzed the different epidemiological and virological variables that can modify the magnitude, function and anatomical localization of SARS-CoV-2-specific T cells and their influence in the ability of T cells to protect the host from severe COVID-19 development. The emergence of SARS-CoV-2 variants capable of evading neutralizing antibodies have increased the interest in defining the immunological correlates of disease protection. Bertoletti, Le Bert, and Tan summarize how SARS-CoV-2-specific T cell magnitude, function and anatomical localization can affect the their ability to protect against severe COVID-19.

Structure deposition and release

Deposited: 2021-08-02
Released: 2022-04-27
Revised: 2022-08-17

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: YLQPRTFLL

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 TYR

TYR171
TYR159
TYR59
TYR7
PHE33
THR163
GLU63
TRP167
LYS66
MET5
P2 LEU

MET45
TYR159
TYR7
VAL67
TYR99
PHE9
LYS66
HIS70
GLU63
P3 GLN

TYR99
LYS66
HIS114
GLN155
HIS70
TYR159
LEU156
ARG97
P4 PRO

LYS66
TYR159
P5 ARG

GLN155
HIS70
ARG97
P6 THR

HIS70
THR73
ALA69
LYS66
P7 PHE

ARG97
TYR116
TRP147
GLN155
ASP77
HIS114
VAL152
LEU156
THR73
P8 LEU

THR143
TRP147
ASP77
LYS146
THR73
VAL76
P9 LEU

LYS146
TYR84
THR143
THR142
THR80
TYR116
LEU81
TRP147
ASP77
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
GLU63
LYS66
TYR7
B Pocket

ALA24
VAL34
MET45
GLU63
LYS66
VAL67
TYR7
HIS70
PHE9
TYR99
C Pocket

HIS70
THR73
HIS74
PHE9
ARG97
D Pocket

HIS114
GLN155
LEU156
TYR159
LEU160
TYR99
E Pocket

HIS114
TRP147
VAL152
LEU156
ARG97
F Pocket

TYR116
TYR123
THR143
LYS146
TRP147
ASP77
THR80
LEU81
TYR84
VAL95

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*02:01
IPD-IMGT/HLA
[ipd-imgt:HLA35266]
        10        20        30        40        50        60
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
        70        80        90       100       110       120
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
       130       140       150       160       170       180
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
       190       200       210       220       230       240
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
       250       260       270
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

3. Peptide
YLQPRTFLL

4. T cell receptor alpha
T cell receptor alpha
TRAV12
        10        20        30        40        50        60
RKEVEQDPGPFNVPEGATVAFNCTYSNSASQSFFWYRQDCRLEPKLIMSVYSSGNEDGRF
        70        80        90       100       110       120
TAQLNRASQYISLLIRDSKLSDSATYLCVVNINTDKLIFGTGTRLQVFPNIQNPDPAVYQ
       130       140       150       160       170       180
LRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
       190       200
ACANAFNNSIIPEDTFFPSPESS

5. T cell receptor beta
T cell receptor beta
TRBV7
        10        20        30        40        50        60
DTGVSQDPRHKITKRGQNVTFRCDPISEHNRLYWYRQTLGQGPEFLTYFQNEAQLEKSRL
        70        80        90       100       110       120
LSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSSANSGELFFGEGSRLTVLEDLKNVF
       130       140       150       160       170       180
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
       190       200       210       220       230       240
ALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG

RAD


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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or in the case of JSON formatted files to retrieve it and use it as part of notebooks such as Jupyter or GoogleColab.
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. 7PBE assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 7PBE assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 7PBE assembly 1  
Peptide only [cif]
  1. 7PBE assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/7pbe

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