9EPA | pdb_00009epa

Crystal structure of DARPin NY_1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 
    0.215 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Development of DARPin T cell engagers for specific targeting of tumor-associated HLA/peptide complexes.

Venetz-Arenas, N.Schulte, T.Muller, S.Wallden, K.Fischer, S.Resink, T.Kadri, N.Paladino, M.Pina, N.Radom, F.Villemagne, D.Bruckmaier, S.Cornelius, A.Hospodarsch, T.Alici, E.Ljunggren, H.G.Chambers, B.J.Han, X.Sun, R.Carroni, M.Levitsky, V.Sandalova, T.Walser, M.Achour, A.

(2025) iScience 28: 113926-113926

  • DOI: https://doi.org/10.1016/j.isci.2025.113926
  • Primary Citation of Related Structures:  
    9EPA, 9FE1

  • PubMed Abstract: 

    The balance between affinity and specificity in T cell receptor (TCR)-dependent targeting of HLA-restricted tumor-associated antigens presents a significant challenge for immunotherapy development. T cell engagers that circumvent these limitations are therefore of particular interest. We established a process to generate bispecific designed ankyrin repeat proteins (DARPins) that simultaneously target HLA-I/peptide complexes and CD3e. These high-affinity T cell engagers elicited CD8 + T cell activation against tumor targets with strong peptide specificity, as confirmed by X-scanning mutagenesis and functional killing assays. A cryo-EM structure of the ternary DARPin/HLA-A∗0201/NY-ESO1 157-165 complex revealed a rigid, concave DARPin surface spanning the full length of the peptide-binding cleft, contacting both α-helices and the peptide. The present findings reveal promising immuno-oncotherapeutic approaches and demonstrate the feasibility of rapidly developing DARPins with high affinity and specificity for HLA/peptide targets, which can be readily combined with a new generation of anti-CD3e-specific DARPins.


  • Organizational Affiliation
    • Molecular Partners AG, Schlieren-Zurich, Switzerland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DARPin NY_1175synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free:  0.215 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.558α = 90
b = 43.284β = 93.784
c = 32.409γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--
CancerfondenSweden--
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references