9QWJ | pdb_00009qwj

Crystal structure of S2c TCR in complex with CD1c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 
    0.235 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Models: experimental
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Literature

A CD1c lipid agnostic T cell receptor bispecific engager redirects T cells against CD1c + cells.

Szoke-Kovacs, R.Khakoo, S.Rangel, V.L.Della Cristina, P.Pentier, J.Khanolkar, R.El-Ajouz, S.Simmons, R.Cole, D.K.Gogolak, P.Salio, M.Karuppiah, V.

(2025) Front Immunol 16: 1614610-1614610

  • DOI: https://doi.org/10.3389/fimmu.2025.1614610
  • Primary Citation of Related Structures:  
    9QWJ, 9QWK

  • PubMed Abstract: 

    Immunotherapy is emerging as an efficacious treatment for some cancers, complementing traditional chemo-radiation therapies. Specific markers at the cell surface of cancer cells can be used as immunotherapy targets. However, many of these markers are defined by a patient's genetic background, limiting their use across the human population. Here, we investigated the non-polymorphic antigen presenting molecule, CD1c, that is only expressed on subsets of mature hematopoietic cells, as a potential immunotherapy target with reduced risk of off-tumor on-target toxicity in healthy tissues. We identified a T cell receptor (TCR) which recognises CD1c in a lipid independent manner and determined the crystal structure of the TCR-CD1c complex which revealed flexibility around the lipid binding region, and a new binding mechanism of auto-antigen recognition. We generated affinity enhanced variants of the TCR and fused them to an anti-CD3 antibody for T cell redirection. Lipidomic analysis revealed promiscuous lipid recognition of CD1c by the affinity enhanced TCR variants, with preference for larger lipid head group, a finding which is supported by the crystal structure. The bispecific molecule induced potent re-directed T cell killing of CD1c positive cell lines. These proof-of-concept findings demonstrate that CD1c targeting TCR bispecific engagers might be good candidates for the development of non-MHC restricted, universal therapeutics for the treatment of CD1c+ leukemias.


  • Organizational Affiliation
    • Experimental Immunology, Immunocore Ltd, Abingdon, United Kingdom.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin,T-cell surface glycoprotein CD1cA [auth B],
D [auth N]
442Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22PCD1C
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Find proteins for P29017 (Homo sapiens)
Explore P29017 
Go to UniProtKB:  P29017
PHAROS:  P29017
GTEx:  ENSG00000158481 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP29017P61769
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P61769-1P29017-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TCR alphaB [auth D],
E [auth T]
199Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
TCR betaC [auth E],
F [auth U]
246Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C],
H [auth F]
2N-Glycosylation
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
J [auth B]
K [auth B]
M [auth B]
N [auth B]
V [auth N]
J [auth B],
K [auth B],
M [auth B],
N [auth B],
V [auth N],
W [auth N]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BMA
Query on BMA

Download Ideal Coordinates CCD File 
L [auth B],
X [auth N]
beta-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
D12 (Subject of Investigation/LOI)
Query on D12

Download Ideal Coordinates CCD File 
O [auth B],
P [auth B]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10 (Subject of Investigation/LOI)
Query on D10

Download Ideal Coordinates CCD File 
AA [auth N],
Z [auth N]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth T]
I [auth B]
Q [auth B]
R [auth D]
T [auth E]
BA [auth T],
I [auth B],
Q [auth B],
R [auth D],
T [auth E],
U [auth N],
Y [auth N]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth T],
DA [auth T],
S [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free:  0.235 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.373α = 90
b = 122.068β = 110.03
c = 108.696γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release