9O9C | pdb_00009o9c

Structure of the IL-18 Surrogate Cytokine Agonist DR3085


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 
    0.291 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structure-Guided Stapling of Dimeric Conformations and Linker Engineering Enhance Thermostability and Fine-Tune Activity of Bispecific VHH Cytokine Agonists.

Trenker, R.Rokkam, D.Morin, A.Balasubrahmanyam, P.Paredes, V.Cheng, I.de Waal Malefyt, R.Oft, M.Lupardus, P.Vivona, S.

(2025) Antibodies (Basel) 14

  • DOI: https://doi.org/10.3390/antib14030074
  • Primary Citation Related Structures: 
    9O99, 9O9A, 9O9B, 9O9C

  • PubMed Abstract: 

    Bispecific antibodies have emerged as a promising class of therapeutics, enabling simultaneous targeting of two distinct antigens. Single-domain antibodies (sdAbs) comprising camelid variable heavy chains (VHHs) provide a compact and adaptable platform for bispecific antibody design due to their small size and ease of linkage. Here we investigate structure-activity relationship of VHH-based cytokine surrogates by combining cell signaling and functional assays with x-ray crystallography and other biophysical techniques. We describe crystal structures of four unique bispecific VHHs that engage and activate the cytokine receptor pairs IL-18Rα/IL-18Rβ and IL-2Rβ/IL-2Rγ. These bispecific VHH molecules, referred to as surrogate cytokine agonists (SCAs), create unique cytokine signals that can be tuned by linker engineering. Our structural analysis reveals multiple dimeric conformations for these bispecific SCAs, where the two VHH domains can interact to form a compact structure. We demonstrate that the dimeric conformation can be enforced via engineering of a non-native disulfide bond between the VHH subunits, thus enhancing molecular thermostability. Our findings have important implications for the design and engineering of bispecific VHHs or sdAbs, offering a novel strategy for tuning their activity and increasing their stability.


  • Organizational Affiliation
    • Department of Discovery, Pharmacology and Translational Research, Synthekine, Menlo Park, CA 94025, USA.

Macromolecule Content 

  • Total Structure Weight: 53.05 kDa 
  • Atom Count: 3,447 
  • Modeled Residue Count: 459 
  • Deposited Residue Count: 500 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
IL-18 Surrogate Cytokine Agonist DR3085A [auth B],
B [auth A]
250Lama glamaMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free:  0.291 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.64α = 90
b = 92.64β = 90
c = 181.846γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
ISOLDEmodel building
Cootmodel building
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

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: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-10-08
    Changes: Database references