9IUT | pdb_00009iut

Crystal structure of cancer-specific anti-HER2 antibody H2Mab-250 in complex with epitope peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Preferential tumor targeting of HER2 by iPSC-derived CAR T cells engineered to overcome multiple barriers to solid tumor efficacy.

Hosking, M.P.Shirinbak, S.Omilusik, K.Chandra, S.Kaneko, M.K.Gentile, A.Yamamoto, S.Shrestha, B.Grant, J.Boyett, M.Cardenas, D.Keegan, H.Ibitokou, S.Pavon, C.Mizoguchi, T.Ihara, T.Nakayama, D.Abujarour, R.Lee, T.T.Clarke, R.Goodridge, J.Peralta, E.Maeda, T.Takagi, J.Arimori, T.Kato, Y.Valamehr, B.

(2025) Cell Stem Cell 32: 1087-1101.e4

  • DOI: https://doi.org/10.1016/j.stem.2025.05.007
  • Primary Citation of Related Structures:  
    9IUT

  • PubMed Abstract: 

    Chimeric antigen receptor (CAR) T cell therapies in solid tumors have been limited by on-target, off-tumor toxicity, antigen heterogeneity, and an inability to simultaneously overcome multiple diverse resistance mechanisms within the tumor microenvironment that attenuate anti-tumor activity. Here, we describe an induced pluripotent stem cell (iPSC)-derived CAR T cell that combines a human epidermal growth factor receptor 2 (HER2)-targeting CAR-differentially recognizing tumor from normal cells and enabling detection of both truncated and misfolded HER2-with multiplex editing designed to address and overcome obstacles to maximize efficacy in solid tumor indications. The iPSC-derived, HER2-directed CAR T cells maintained potent HER2-specific anti-tumor activity in both in vitro and in vivo settings, with limited cytolytic targeting of HER2+ normal targets. Combination with therapeutic antibodies enabled comprehensive multi-antigen targeting through both the CAR and a high-affinity, non-cleavable CD16a Fc receptor. Additionally, specific engineering of interleukin (IL)-7R-fusion, transforming growth factor β (TGF-β)-IL-18R, and CXCR2 enabled sustained persistence, resistance to TGF-β-mediated suppression, and specific migration to the tumor.


  • Organizational Affiliation
    • Fate Therapeutics, Inc., San Diego, CA, USA. Electronic address: martin.hosking@fatetherapeutics.com.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H2Mab-250 VH(S112C)-SARAH
A, D
169Mus musculusMutation(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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H2Mab-250 VL-SARAH(S37C)
B, E
171Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
H2Mab-250 epitope peptide
C, F
8Homo sapiensMutation(s): 0 
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens)
Explore P04626 
Go to UniProtKB:  P04626
PHAROS:  P04626
GTEx:  ENSG00000141736 
Entity Groups  
UniProt GroupP04626
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.545α = 90
b = 123.199β = 90
c = 96.083γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H02416

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Database references
  • Version 1.2: 2025-07-16
    Changes: Database references