7Q98

MHC Class I A02 Allele presenting NLSALGIFST


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Targeting of multiple tumor-associated antigens by individual T cell receptors during successful cancer immunotherapy.

Dolton, G.Rius, C.Wall, A.Szomolay, B.Bianchi, V.Galloway, S.A.E.Hasan, M.S.Morin, T.Caillaud, M.E.Thomas, H.L.Theaker, S.Tan, L.R.Fuller, A.Topley, K.Legut, M.Attaf, M.Hopkins, J.R.Behiry, E.Zabkiewicz, J.Alvares, C.Lloyd, A.Rogers, A.Henley, P.Fegan, C.Ottmann, O.Man, S.Crowther, M.D.Donia, M.Svane, I.M.Cole, D.K.Brown, P.E.Rizkallah, P.Sewell, A.K.

(2023) Cell 186: 3333-3349.e27

  • DOI: https://doi.org/10.1016/j.cell.2023.06.020
  • Primary Citation of Related Structures:  
    7Q98, 7Q99, 7Q9A, 7Q9B, 7ZUC

  • PubMed Abstract: 

    The T cells of the immune system can target tumors and clear solid cancers following tumor-infiltrating lymphocyte (TIL) therapy. We used combinatorial peptide libraries and a proteomic database to reveal the antigen specificities of persistent cancer-specific T cell receptors (TCRs) following successful TIL therapy for stage IV malignant melanoma. Remarkably, individual TCRs could target multiple different tumor types via the HLA A 02:01-restricted epitopes EAAGIGILTV, LLLGIGILVL, and NLSALGIFST from Melan A, BST2, and IMP2, respectively. Atomic structures of a TCR bound to all three antigens revealed the importance of the shared x-x-x-A/G-I/L-G-I-x-x-x recognition motif. Multi-epitope targeting allows individual T cells to attack cancer in several ways simultaneously. Such "multipronged" T cells exhibited superior recognition of cancer cells compared with conventional T cell recognition of individual epitopes, making them attractive candidates for the development of future immunotherapies.


  • Organizational Affiliation

    Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales CF14 4XN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen
A, D, G, J, M
276Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for A0A140T913 (Homo sapiens)
Explore A0A140T913 
Go to UniProtKB:  A0A140T913
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140T913
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E, H, K, N
100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ASN-LEU-SER-ALA-LEU-GLY-ILE-PHE-SER-THR
C, F, I, L, O
10Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6M1 (Homo sapiens)
Explore Q9Y6M1 
Go to UniProtKB:  Q9Y6M1
PHAROS:  Q9Y6M1
GTEx:  ENSG00000073792 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6M1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
AB [auth N]
GA [auth E]
JA [auth G]
KA [auth G]
LA [auth G]
AB [auth N],
GA [auth E],
JA [auth G],
KA [auth G],
LA [auth G],
P [auth A],
Q [auth A],
QA [auth H],
SA [auth J],
T [auth B],
V [auth D],
VA [auth K],
W [auth D],
X [auth D],
ZA [auth N]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
BB [auth N]
CA [auth D]
DA [auth D]
AA [auth D],
BA [auth D],
BB [auth N],
CA [auth D],
DA [auth D],
EA [auth D],
HA [auth E],
IA [auth E],
MA [auth G],
NA [auth G],
OA [auth G],
PA [auth G],
R [auth A],
RA [auth H],
S [auth A],
TA [auth J],
UA [auth J],
WA [auth K],
XA [auth K],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CB [auth N],
FA [auth D],
U [auth B],
YA [auth M]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.247α = 90
b = 169.693β = 90
c = 248.827γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-02-07
    Changes: Refinement description