7RE7

TCR mimic antibody (Fab fragment) in complex with AFP/HLA-A*02


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinoma.

Liu, C.Liu, H.Dasgupta, M.Hellman, L.M.Zhang, X.Qu, K.Xue, H.Wang, Y.Fan, F.Chang, Q.Yu, D.Ge, L.Zhang, Y.Cui, Z.Zhang, P.Heller, B.Zhang, H.Shi, B.Baker, B.M.Liu, C.

(2022) Sci Rep 12: 12068-12068

  • DOI: https://doi.org/10.1038/s41598-022-15946-5
  • Primary Citation of Related Structures:  
    7RE7, 7RE8, 7RE9

  • PubMed Abstract: 

    Monoclonal antibodies are at the vanguard of the most promising cancer treatments. Whereas traditional therapeutic antibodies have been limited to extracellular antigens, T cell receptor mimic (TCRm) antibodies can target intracellular antigens presented by cell surface major histocompatibility complex (MHC) proteins. TCRm antibodies can therefore target a repertoire of otherwise undruggable cancer antigens. However, the consequences of off-target peptide/MHC recognition with engineered T cell therapies are severe, and thus there are significant safety concerns with TCRm antibodies. Here we explored the specificity and safety profile of a new TCRm-based T cell therapy for hepatocellular carcinoma (HCC), a solid tumor for which no effective treatment exists. We targeted an alpha-fetoprotein peptide presented by HLA-A*02 with a highly specific TCRm, which crystallographic structural analysis showed binds directly over the HLA protein and interfaces with the full length of the peptide. We fused the TCRm to the γ and δ subunits of a TCR, producing a signaling AbTCR construct. This was combined with an scFv/CD28 co-stimulatory molecule targeting glypican-3 for increased efficacy towards tumor cells. This AbTCR + co-stimulatory T cell therapy showed potent activity against AFP-positive cancer cell lines in vitro and an in an in vivo model and undetectable activity against AFP-negative cells. In an in-human safety assessment, no significant adverse events or cytokine release syndrome were observed and evidence of efficacy was seen. Remarkably, one patient with metastatic HCC achieved a complete remission after nine months and ultimately qualified for a liver transplant.


  • Organizational Affiliation

    The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chainA [auth I],
C [auth H]
224Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chainB [auth J],
D [auth L]
216Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigenE [auth A],
G [auth D]
295Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for A0A140T913 (Homo sapiens)
Explore A0A140T913 
Go to UniProtKB:  A0A140T913
Entity Groups  
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UniProt GroupA0A140T913
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinF [auth B],
H [auth E]
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  
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UniProt GroupP61769
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  • Reference Sequence

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PHE-MET-ASN-LYS-PHE-ILE-TYR-GLU-ILEI [auth C],
J [auth F]
9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02771 (Homo sapiens)
Explore P02771 
Go to UniProtKB:  P02771
PHAROS:  P02771
GTEx:  ENSG00000081051 
Entity Groups  
UniProt GroupP02771
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P6G
Query on P6G

Download Ideal Coordinates CCD File 
S [auth B]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
K [auth I],
M [auth H],
T [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
1PE (Subject of Investigation/LOI)
Query on 1PE

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V [auth D]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

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Q [auth A],
R [auth A],
Y [auth D],
Z [auth E]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
AA [auth E],
U [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL
Query on GOL

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BA [auth E]
CA [auth E]
L [auth I]
N [auth H]
O [auth H]
BA [auth E],
CA [auth E],
L [auth I],
N [auth H],
O [auth H],
P [auth A],
X [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT
Query on FMT

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W [auth D]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.707α = 90
b = 200.912β = 90
c = 244.574γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Derived calculations
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description