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6L9K

Truncated H2-Ld binding "SPSYAYHQF" at 1.80Å 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.

Publication

Structures suggest an approach for converting weak self-peptide tumor antigens into superagonists for CD8 T cells in cancer.

Wei P, Jordan KR, Buhrman JD, Lei J, Deng H, Marrack P, Dai S, Kappler JW, Slansky JE, Yin L
Proc Natl Acad Sci U S A (2021) 118, [doi:10.1073/pnas.2100588118]  [pubmed:34074778

Tumors frequently express unmutated self-tumor-associated antigens (self-TAAs). However, trial results using self-TAAs as vaccine targets against cancer are mixed, often attributed to deletion of T cells with high-affinity receptors (TCRs) for self-TAAs during T cell development. Mutating these weak self-TAAs to produce higher affinity, effective vaccines is challenging, since the mutations may not benefit all members of the broad self-TAA-specific T cell repertoire. We previously identified a common weak murine self-TAA that we converted to a highly effective antitumor vaccine by a single amino acid substitution. In this case the modified and natural self-TAAs still raised very similar sets of CD8 T cells. Our structural studies herein show that the modification of the self-TAA resulted in a subtle change in the major histocompatibility complex I-TAA structure. This amino acid substitution allowed a dramatic conformational change in the peptide during subsequent TCR engagement, creating a large increase in TCR affinity and accounting for the efficacy of the modified self-TAA as a vaccine. These results show that carefully selected, well-characterized modifications to a poorly immunogenic self-TAA can rescue the immune response of the large repertoire of weakly responding natural self-TAA-specific CD8 T cells, driving them to proliferate and differentiate into functional effectors. Subsequently, the unmodified self-TAA on the tumor cells, while unable to drive this response, is nevertheless a sufficient target for the CD8 cytotoxic effectors. Our results suggest a pathway for more efficiently identifying variants of common self-TAAs, which could be useful in vaccine development, complementing other current nonantigen-specific immunotherapies.

Structure deposition and release

Deposited: 2019-11-10
Released: 2020-11-18
Revised: 2021-06-16

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: SPSYAYHQF

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 SER

TYR171
TYR159
TYR59
TYR7
GLU163
ARG62
ILE66
ILE63
TRP167
MET5
P2 PRO

TYR99
TYR45
TYR7
GLU163
ILE66
ILE63
TYR159
P3 SER

ARG97
GLN70
GLU114
TYR99
TYR159
GLU9
ILE66
P4 TYR

ILE66
GLY69
ARG97
GLN70
TYR155
GLN65
TYR156
P5 ALA

TRP73
TYR155
TYR156
PHE116
ARG97
GLN70
P6 TYR

GLN70
TRP73
TYR155
TYR156
P7 HIS

ALA150
GLY151
ASN77
TRP73
ALA152
TRP147
TYR155
TYR156
P8 GLN

TRP147
VAL76
ASN77
LYS146
TRP73
THR143
P9 PHE

ASN77
TRP73
TYR84
THR80
LYS146
TRP147
THR143
PHE116
ILE124
LEU81
LEU95
ILE142
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
GLU163
TRP167
TYR171
MET5
TYR59
ILE63
ILE66
TYR7
B Pocket

SER24
VAL34
TYR45
ILE63
ILE66
ALA67
TYR7
GLN70
GLU9
TYR99
C Pocket

GLN70
TRP73
PHE74
GLU9
ARG97
D Pocket

GLU114
TYR155
TYR156
TYR159
LEU160
TYR99
E Pocket

GLU114
TRP147
ALA152
TYR156
ARG97
F Pocket

PHE116
TYR123
THR143
LYS146
TRP147
ASN77
THR80
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. Class I alpha
H2-Ld
        10        20        30        40        50        60
GPHSMRYYETATSRRGLGEPRYTSVGYVDDKEFVRFDSDAENPRYEPQVPWMEQEGPEYW
        70        80        90       100       110       120
ERITQIAKGQEQWFRVNLRTLLGYYNQSAGGTHTLQRMYGCDVGSDGRLLRGYEQFAYDG
       130       140       150       160       170
CDYIALNEDLRTWTAADMAAQITRRKWEQAGAAEYYRAYLEGECVEWLHRYLKNG

2. Peptide
SPSYAYHQF


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. 6L9K assembly 1  

Components

MHC Class I alpha chain [cif]
  1. 6L9K assembly 1  
MHC Class I antigen binding domain (alpha1/alpha2) [cif]
  1. 6L9K assembly 1  
Peptide only [cif]
  1. 6L9K assembly 1  

Derived data

Data for this page [json]
https://api.histo.fyi/v1/structures/6l9k

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