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 8OZ3 | pdb_00008oz3

Crystal structure of scFv ATOR 1017 bound to human 4-1BB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.271 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.216 (DCC) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8OZ3

This is version 1.1 of the entry. See complete history. 

Literature

ATOR-1017 (evunzekibart), an Fc-gamma receptor conditional 4-1BB agonist designed for optimal safety and efficacy, activates exhausted T cells in combination with anti-PD-1.

Enell Smith, K., Fritzell, S., Nilsson, A., Barchan, K., Rosen, A., Schultz, L., Varas, L., Sall, A., Rose, N., Hakansson, M., von Schantz, L., Ellmark, P.

(2023) Cancer Immunol Immunother 72: 4145-4159

  • DOI: https://doi.org/10.1007/s00262-023-03548-7
  • Primary Citation Related Structures: 
    8OZ3

  • PubMed Abstract: 

    4-1BB (CD137) is a co-stimulatory receptor highly expressed on tumor reactive effector T cells and NK cells, which upon stimulation prolongs persistence of tumor reactive effector T and NK cells within the tumor and induces long-lived memory T cells. 4-1BB agonistic antibodies have been shown to induce strong anti-tumor effects that synergize with immune checkpoint inhibitors. The first generation of 4-1BB agonists was, however, hampered by dose-limiting toxicities resulting in suboptimal dose levels or poor agonistic activity. ATOR-1017 (evunzekibart), a second-generation Fc-gamma receptor conditional 4-1BB agonist in IgG4 format, was designed to overcome the limitations of the first generation of 4-1BB agonists, providing strong agonistic effect while minimizing systemic immune activation and risk of hepatoxicity. The epitope of ATOR-1017 was determined by X-ray crystallography, and the functional activity was assessed in vitro and in vivo as monotherapy or in combination with anti-PD1. ATOR-1017 binds to a unique epitope on 4-1BB enabling ATOR-1017 to activate T cells, including cells with an exhausted phenotype, and NK cells, in a cross-linking dependent, FcγR-conditional, manner. This translated into a tumor-directed and potent anti-tumor therapeutic effect in vivo, which was further enhanced with anti-PD-1 treatment. These preclinical data demonstrate a strong safety profile of ATOR-1017, together with its potent therapeutic effect as monotherapy and in combination with anti-PD1, supporting further clinical development of ATOR-1017.


  • Organizational Affiliation: 
    • Alligator Bioscience AB, Lund, Sweden.

Macromolecule Content 

  • Total Structure Weight: 126.34 kDa 
  • Atom Count: 5,473 
  • Modeled Residue Count: 725 
  • Deposited Residue Count: 1,174 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Single chain FvA,
E [auth H]
230Homo sapiensMutation(s): 0 
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Single chain FvB,
F [auth L]
216Homo sapiensMutation(s): 0 
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 9
C, D
141Homo sapiensMutation(s): 0 
Gene Names: TNFRSF9, CD137, ILA
UniProt & NIH Common Fund Data Resources
Find proteins for Q07011 (Homo sapiens)
Explore Q07011 
Go to UniProtKB:  Q07011
PHAROS:  Q07011
GTEx:  ENSG00000049249 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07011
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.271 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.216 (DCC) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.923α = 90
b = 125.214β = 90
c = 128.785γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoXDSdata reduction
autoXDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary