9QWK | pdb_00009qwk

Crystal structure of S2c-a5b6 TCR in complex with CD1c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.253 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.227 (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 CD1c442Homo 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: 1Go to GlyGen: P29017-1P61769-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TCR alphaC [auth D],
G [auth H],
K [auth M],
O [auth R]
200Homo 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 betaD [auth E],
E [auth F],
I [auth K],
M [auth P]
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
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseQ [auth C],
S [auth N]
2N-Glycosylation
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseR [auth I]2N/A
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseT [auth S]4N-Glycosylation
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
U, V
3N-Glycosylation
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CA [auth L],
HA [auth Q]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUC
Query on FUC

Download Ideal Coordinates CCD File 
GA [auth O]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
D10 (Subject of Investigation/LOI)
Query on D10

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth L]
EA [auth L]
IA [auth Q]
JA [auth Q]
AA [auth G],
DA [auth L],
EA [auth L],
IA [auth Q],
JA [auth Q],
W [auth A],
X [auth A],
Z [auth G]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
BA [auth H],
FA [auth M],
KA [auth R],
Y [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.253 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.233α = 91.85
b = 83.652β = 95.99
c = 180.13γ = 115.61
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data 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