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5TS1

H2-Kd binding "YYQSGLSIV" at 2.30Å 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', 'D', 'F', 'H']
2. Class I alpha
H2-Kd
['A', 'C', 'E', 'G']
3. Peptide
YYQSGLSIV
['P', 'Q', 'R', 'S']

Species


Locus / Allele group


Publication

MHC-restricted Ag85B-specific CD8+ T��cells are enhanced by recombinant BCG prime and DNA boost immunization in mice.

Komine-Aizawa S, Jiang J, Mizuno S, Hayakawa S, Matsuo K, Boyd LF, Margulies DH, Honda M
Eur. J. Immunol. (2019) [doi:10.1002/eji.201847988]  [pubmed:31135967

Despite efforts to develop effective treatments and vaccines, Mycobacterium tuberculosis (Mtb), particularly pulmonary Mtb, continues to provide major health challenges worldwide. To improve immunization against the persistent health challenge of Mtb infection, we have studied the CD8+ T cell response to Bacillus Calmette-Guérin (BCG) and recombinant BCG (rBCG) in mice. Here, we generated CD8+ T cells with an rBCG-based vaccine encoding the Ag85B protein of M. kansasii, termed rBCG-Mkan85B, followed by boosting with plasmid DNA expressing the Ag85B gene (DNA-Mkan85B). We identified two MHC-I (H2-Kd )-restricted epitopes that induce cross-reactive responses to Mtb and other related mycobacteria in both BALB/c (H2d ) and CB6F1 (H2b/d ) mice. The H2-Kd -restricted peptide epitopes elicited polyfunctional CD8+ T cell responses that were also highly cross-reactive with those of other proteins of the Ag85 complex. Tetramer staining indicated that the two H2-Kd -restricted epitopes elicit distinct CD8+ T cell populations, a result explained by the X-ray structure of the two peptide/H2-Kd complexes. These results suggest that rBCG-Mkan85B vector-based immunization and DNA-Mkan85B boost may enhance CD8+ T cell response to Mtb, and might help to overcome the limited effectiveness of the current BCG in eliciting tuberculosis immunity.

Structure deposition and release

Deposited: 2016-10-27
Released: 2018-05-09
Revised: 2020-02-05

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: YYQSGLSIV

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

ARG66
LEU5
GLN63
TRP167
TYR59
TYR7
PHE99
GLU62
TYR171
TYR159
GLU163
P2 TYR

PHE74
TYR7
PHE99
ARG97
ALA67
TYR159
PHE22
PHE45
VAL9
ARG66
ASP70
ALA24
GLN63
P3 GLN

TYR155
ARG66
PHE99
TYR156
ARG97
TYR159
ASP70
P4 SER

SER69
ARG97
TYR155
ARG66
ASP70
TYR156
P5 GLY

TYR156
ARG97
TRP73
ASP70
TYR155
P6 LEU

TRP73
ALA150
TYR155
GLY151
ASP152
TYR156
P7 SER

TYR156
TRP147
ALA150
TRP73
ASP152
LYS146
P8 ILE

TRP73
VAL76
THR80
TRP147
SER77
LYS146
P9 VAL

ILE142
ALA81
TYR123
THR80
TRP147
TRP73
SER77
TYR84
LYS146
PHE95
THR143

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

LEU159
CYS163
LEU167
LEU171
ARG5
TRP59
THR63
ALA66
PHE7
B Pocket

VAL24
ARG34
GLU45
THR63
ALA66
LYS67
PHE7
GLU70
THR9
GLY99
C Pocket

GLU70
PHE73
ARG74
THR9
MET97
D Pocket

GLN114
TYR155
ARG156
LEU159
GLU160
GLY99
E Pocket

GLN114
GLU147
ALA152
ARG156
MET97
F Pocket

ALA116
ILE123
ARG143
TRP146
GLU147
LEU77
ALA80
GLN81
TYR84
GLN95

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
H2-Kd
        10        20        30        40        50        60
PHSLRYFVTAVSRPGLGEPRFIAVGYVDDTQFVRFDSDADNPRFEPRAPWMEQEGPEYWE
        70        80        90       100       110       120
EQTQRAKSDEQWFRVSLRTAQRYYNQSKGGSHTFQRMFGCDVGSDWRLLRGYHQFAYDGR
       130       140       150       160       170       180
DYIALNEDLKTWTAADTAALITRRKWEQAGDAEYYRAYLEGECVEWLRRYLELGNETLLR
       190       200       210       220       230       240
TDSPKAHVTYHPRSQVDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGTF
       250       260       270
QKWAAVVVPLGKEQNYTCHVHHKGLPEPLTLRWKP

3. Peptide
YYQSGLSIV


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. 5TS1 assembly 1  
  2. 5TS1 assembly 2  
  3. 5TS1 assembly 3  
  4. 5TS1 assembly 4  

Components

MHC Class I alpha chain [cif]
  1. 5TS1 assembly 1  
  2. 5TS1 assembly 2  
  3. 5TS1 assembly 3  
  4. 5TS1 assembly 4  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 5TS1 assembly 1  
  2. 5TS1 assembly 2  
  3. 5TS1 assembly 3  
  4. 5TS1 assembly 4  
Peptide only [cif]
  1. 5TS1 assembly 1  
  2. 5TS1 assembly 2  
  3. 5TS1 assembly 3  
  4. 5TS1 assembly 4  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/5ts1

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