7WKJ
HLA-A*11:01 binding "KTFPPTEPK" at 1.50Å 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
- Publication
- Peptide details
- Peptide neighbours
- Binding cleft pockets
- Chain sequences
- Downloadable data
- Data license
- Footnotes
Complex type
1. Beta 2 microglobulin
['B']
2. Class I alpha
HLA-A*11:01
HLA-A*11:01
['A']
3. Peptide
KTFPPTEPK
KTFPPTEPK
['C']
Species
Locus / Allele group
A COVID-19 T-Cell Response Detection Method Based on a Newly Identified Human CD8+ T Cell Epitope from SARS-CoV-2 - Hubei Province, China, 2021.
Zhang J, Lu D, Li M, Liu M, Yao S, Zhan J, Liu WJ, Gao GF
China CDC Wkly (2022) 4,
83-87 [doi:10.46234/ccdcw2021.258]
[pubmed:35186375]
Introduction
Similar to antibody detection, severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2)-specific T-cell response evaluation is also pivotal among the coronavirus disease 2019 (COVID-19) convalescents and the vaccinated populations. Nucleocapsid (N) protein is one of the main structural proteins of SARS-CoV-2 and can trigger T-cell responses in humans.Methods
An overlapping peptide pool covering the full length of the N protein was designed, peptides with positive T-cell activating potency in COVID-19 convalescents were screened, and CD8+ T cell epitopes were further identified. The epitope was used to detect the SARS-CoV-2-specific CD8+ T cell responses in COVID-19 convalescents based in intracellular cytokine staining and tetramer staining in flow cytometry.Results
A human leukocyte antigen A (HLA-A)*1101-restricted CD8+ T cell epitope, which could stimulate the production of IFN-γ via peripheral blood mononuclear cells (PBMCs) of the convalescents was defined, and the tetramer generated with this epitope could detect SARS-CoV-2-specific T cells in the PBMCs of the convalescents. The structural investigation eliminated that the epitope was a typical HLA-A*1101-restricted T-cell epitope which was conserved among all the sarbecoviruses.Discussion
The newly identified SARS-CoV-2-derived T-cell epitope was helpful to detect the cellular immunity against different sarbecoviruses including SARS-CoV and SARS-CoV-2. This study provided an evaluation method and also a peptide candidate for the research and development of T-cell based vaccine for the virus.Structure deposition and release
Deposited: 2022-01-10
Released: 2022-03-02
Revised: 2022-03-09
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
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
LYS
ARG163
GLU63
MET5
TYR171
TYR159
TRP167
GLN62
TYR59
TYR7
GLU58
|
P2
THR
TYR9
MET45
TYR99
GLU63
VAL67
TYR159
TYR7
ASN66
|
P3
PHE
GLN155
TYR159
ASN66
TYR9
ARG114
TYR99
GLN156
|
P4
PRO
TYR159
ASN66
GLN70
|
P5
PRO
ASN66
THR73
ALA69
GLN70
|
P6
THR
ARG114
ASP77
ASP74
THR73
ILE97
GLN70
|
P7
GLU
ALA152
GLN155
ALA150
THR73
TRP147
ASP77
|
P8
PRO
LYS146
THR73
TRP147
ASP77
THR143
|
P9
LYS
ILE142
TRP147
ASP77
TYR84
ASP116
LEU81
THR80
ARG114
THR143
LYS146
ILE97
TYR123
ILE95
ILE124
|
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]
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.
|
1. Beta 2 microglobulin
Beta 2 microglobulin
|
10 20 30 40 50 60
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW 70 80 90 SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM |
|
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
|
KTFPPTEPK
|
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
Data can be downloaded to your local machine from the links below.
Clicking on the clipboard icon will copy the url for the data to your clipboard.
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e.g. load http://www.histo.fyi/structures/downloads/1hhk_1_peptide.cif
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.
Components
MHC Class I alpha chain [cif]
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
Peptide only [cif]
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
- 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.