6R2L

NYBR1-A2-SLSKILDTV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Specificity of bispecific T cell receptors and antibodies targeting peptide-HLA.

Holland, C.J.Crean, R.M.Pentier, J.M.de Wet, B.Lloyd, A.Srikannathasan, V.Lissin, N.Lloyd, K.A.Blicher, T.H.Conroy, P.J.Hock, M.Pengelly, R.J.Spinner, T.E.Cameron, B.Potter, E.A.Jeyanthan, A.Molloy, P.E.Sami, M.Aleksic, M.Liddy, N.Robinson, R.A.Harper, S.Lepore, M.Pudney, C.R.van der Kamp, M.W.Rizkallah, P.J.Jakobsen, B.K.Vuidepot, A.Cole, D.K.

(2020) J Clin Invest 130: 2673-2688

  • DOI: https://doi.org/10.1172/JCI130562
  • Primary Citation of Related Structures:  
    6R2L, 6RSY

  • PubMed Abstract: 

    Tumor-associated peptide-human leukocyte antigen complexes (pHLAs) represent the largest pool of cell surface-expressed cancer-specific epitopes, making them attractive targets for cancer therapies. Soluble bispecific molecules that incorporate an anti-CD3 effector function are being developed to redirect T cells against these targets using 2 different approaches. The first achieves pHLA recognition via affinity-enhanced versions of natural TCRs (e.g., immune-mobilizing monoclonal T cell receptors against cancer [ImmTAC] molecules), whereas the second harnesses an antibody-based format (TCR-mimic antibodies). For both classes of reagent, target specificity is vital, considering the vast universe of potential pHLA molecules that can be presented on healthy cells. Here, we made use of structural, biochemical, and computational approaches to investigate the molecular rules underpinning the reactivity patterns of pHLA-targeting bispecifics. We demonstrate that affinity-enhanced TCRs engage pHLA using a comparatively broad and balanced energetic footprint, with interactions distributed over several HLA and peptide side chains. As ImmTAC molecules, these TCRs also retained a greater degree of pHLA selectivity, with less off-target activity in cellular assays. Conversely, TCR-mimic antibodies tended to exhibit binding modes focused more toward hot spots on the HLA surface and exhibited a greater degree of crossreactivity. Our findings extend our understanding of the basic principles that underpin pHLA selectivity and exemplify a number of molecular approaches that can be used to probe the specificity of pHLA-targeting molecules, aiding the development of future reagents.


  • Organizational Affiliation

    Immunocore Ltd., Milton Park, Abingdon, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A-2 alpha chain276Homo sapiensMutation(s): 0 
Gene Names: HLA-AHLAA
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Find proteins for P04439 (Homo sapiens)
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PHAROS:  P04439
GTEx:  ENSG00000206503 
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UniProt GroupP04439
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin100Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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Find proteins for P61769 (Homo sapiens)
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PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL9Homo sapiensMutation(s): 0 
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PHAROS:  Q9BXX3
GTEx:  ENSG00000148513 
Entity Groups  
UniProt GroupQ9BXX3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor alpha variable 22,Human nkt tcr alpha chain194Homo sapiensMutation(s): 0 
Gene Names: TRAV22B2MHDCMA22P
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Find proteins for A0A0B4J277 (Homo sapiens)
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PHAROS:  A0A0B4J277
GTEx:  ENSG00000211802 
Find proteins for K7N5M3 (Homo sapiens)
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UniProt GroupsK7N5M3A0A0B4J277
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
T cell receptor beta variable 11-2,Human nkt tcr beta chain247Homo sapiensMutation(s): 0 
Gene Names: TRBV11-2TCRBV21S3A2N2TB2MHDCMA22P
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PHAROS:  A0A584
Find proteins for K7N5M4 (Homo sapiens)
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UniProt GroupsK7N5M4A0A584
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
O [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
K [auth A]
L [auth A]
M [auth A]
N [auth A]
P [auth B]
K [auth A],
L [auth A],
M [auth A],
N [auth A],
P [auth B],
Q [auth B],
R [auth D],
T [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
S [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.21α = 90
b = 99.33β = 90.5
c = 111.44γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-26
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary