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 7P3I | pdb_00007p3i

Crystal structure of human CD40/TNFRSF5 in complex with the anti-CD40 DARPin protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 
    0.253 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 7P3I

This is version 1.2 of the entry. See complete history. 

Literature

A Multispecific Anti-CD40 DARPin Construct Induces Tumor-Selective CD40 Activation and Tumor Regression.

Rigamonti, N., Veitonmaki, N., Domke, C., Barsin, S., Jetzer, S., Abdelmotaleb, O., Bessey, R., Lekishvili, T., Malvezzi, F., Gachechiladze, M., Behe, M., Levitsky, V., Trail, P.A.

(2022) Cancer Immunol Res 10: 626-640

  • DOI: https://doi.org/10.1158/2326-6066.CIR-21-0553
  • Primary Citation Related Structures: 
    7P3I

  • PubMed Abstract: 

    The CD40 receptor is an attractive target for cancer immunotherapy. Although a modest pharmacodynamic effect is seen in patients following administration of CD40-targeting monoclonal antibodies (mAb), the doses that could be safely administered do not result in a meaningful clinical response, most likely due to the limited therapeutic window associated with systemic CD40 activation. To overcome this issue, we developed a multispecific DARPin construct, α-FAPxCD40, which has conditional activity at the site of disease. α-FAPxCD40 activation of CD40 depends on binding to fibroblast activation protein (FAP), a cell-surface protease overexpressed in the stroma of solid tumors. In vitro studies demonstrated that α-FAPxCD40 potently activates human antigen-presenting cells in the presence, but not in the absence, of FAP-positive cells. After intravenous injection, a murine surrogate construct (α-mFAPxCD40) accumulated in FAP-positive tumors, elicited rejection of 88% of these tumors, and induced memory antitumor immunity. Importantly, in contrast to the mouse anti-CD40 tested in parallel, the in vivo antitumor activity of α-mFAPxCD40 was associated neither with elevated blood cytokines nor with hepatotoxicity, both of which contribute to the clinical dose-limiting toxicities of several CD40 mAb. This study demonstrates that α-(m)FAPxCD40 engages CD40 in an FAP-restricted manner, leading to tumor eradication without signs of peripheral toxicity. This distinct preclinical profile suggests that a favorable therapeutic index may be achieved in humans. It further supports the development of α-FAPxCD40, currently tested in a first-in-human clinical study in patients with solid tumors (NCT05098405).


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

Macromolecule Content 

  • Total Structure Weight: 72.84 kDa 
  • Atom Count: 5,104 
  • Modeled Residue Count: 648 
  • Deposited Residue Count: 672 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 5
A, C
177Homo sapiensMutation(s): 0 
Gene Names: CD40, TNFRSF5
UniProt & NIH Common Fund Data Resources
Find proteins for P25942 (Homo sapiens)
Explore P25942 
Go to UniProtKB:  P25942
PHAROS:  P25942
GTEx:  ENSG00000101017 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25942
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Darpin
B, D
159synthetic constructMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.67α = 90
b = 59.564β = 106.99
c = 81.842γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary