8Q3J | pdb_00008q3j

Crystal structure of mIL-38 in complex with a neutralizing Fab e04 fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.283 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8Q3J

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Neutralizing IL-38 activates gamma delta T cell-dependent antitumor immunity and sensitizes for chemotherapy.

da Silva, P.Mora, J.You, X.Wiechmann, S.Putyrski, M.Garcia-Pardo, J.Kannt, A.Ernst, A.Bruene, B.Weigert, A.

(2024) J Immunother Cancer 12

  • DOI: https://doi.org/10.1136/jitc-2023-008641
  • Primary Citation Related Structures: 
    8Q3J

  • PubMed Abstract: 

    The interleukin (IL)-1-family receptor antagonist IL-38 has emerged as a negative regulator of auto-inflammation. Given the intricate interplay between antitumor immunity and auto-inflammation, we hypothesized that blocking IL-38 may enhance tumor immune control. Our hypothesis was tested in the transgenic polyoma virus middle T oncoprotein mammary carcinoma model that is suitable for identifying strong immunomodulators. To investigate the effect of acute IL-38 blockade, we used a neutralizing antibody, alone or in combination with chemotherapy. Immune cell composition and location in tumors were determined by flow cytometry and immunohistochemistry, respectively. The role of γδ T cells was studied using an antibody blocking γδ T-cell receptor signaling. Whole transcriptome RNA sequencing and RNA expression analysis were employed to determine mechanisms downstream of IL-38 neutralization. Additionally, in vitro assays with γδ T cells, CD8+ T cells and cDC1, followed by in vivo CD8+ T cell depletion, were performed to study the underlying mechanistic pathways. Both, genetic ablation of IL-38 and neutralization with the antibody, reduced tumorigenesis, and IL-38 blockade improved chemotherapy efficacy. This was accompanied by an augmented lymphocyte infiltrate dominated by γδ T cells and CD8+ T cells, and signaling through the γδ-T-cell receptor was required for CD8+ T cell infiltration. Rather than directly interacting with CD8+ T cells, γδ T cells recruited conventional dendritic cells (cDC1) into tumors via the chemokine Xcl1. cDC1 in turn activated CD8+ T cells via the Notch pathway. Moreover, IL-38 negatively correlated with cDC1, XCL1-producing γδ T cells, T-cell infiltrates and survival in patients with mammary carcinoma. These data suggest that interfering with IL-38 improves antitumor immunity even in immunologically cold tumors.


  • Organizational Affiliation
    • Faculty of Medicine, Institute of Biochemistry I, Goethe-University Frankfurt, Frankfurt, Germany.

Macromolecule Content 

  • Total Structure Weight: 135.07 kDa 
  • Atom Count: 8,922 
  • Modeled Residue Count: 1,147 
  • Deposited Residue Count: 1,232 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Interleukin-1 family member 10
A, D
152Mus musculusMutation(s): 0 
Gene Names: Il1f10
UniProt
Find proteins for Q8R459 (Mus musculus)
Explore Q8R459 
Go to UniProtKB:  Q8R459
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8R459
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab e04 Light Chain (e04 LC)
B, E
223Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab e04 Heavy Chain (e04 HC)
C, F
241Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.283 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.8α = 90
b = 66.94β = 104.727
c = 129.05γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHENIXrefinement
MxCuBEdata collection
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGermanyFraunhofer Institute for Molecular Biology and Applied Ecology IME

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Structure summary