8DQ6

Structure of A. thaliana MIF/D-DT-like protein-1 (MDL1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Plant MDL proteins synergize with the cytokine MIF at CXCR2 and CXCR4 receptors in human cells.

Spiller, L.Manjula, R.Leissing, F.Basquin, J.Bourilhon, P.Sinitski, D.Brandhofer, M.Levecque, S.Gerra, S.Sabelleck, B.Zhang, L.Feederle, R.Flatley, A.Hoffmann, A.Panstruga, R.Bernhagen, J.Lolis, E.

(2023) Sci Signal 16: eadg2621-eadg2621

  • DOI: https://doi.org/10.1126/scisignal.adg2621
  • Primary Citation of Related Structures:  
    8DQ6, 8DQA

  • PubMed Abstract: 

    Mammalian macrophage migration inhibitory factor (MIF) and its paralog, D-dopachrome tautomerase, are multifunctional inflammatory cytokines. Plants have orthologous MIF and D-dopachrome tautomerase-like (MDL) proteins that mimic some of the effects of MIF on immune cells in vitro. We explored the structural and functional similarities between the three Arabidopsis thaliana MDLs and MIF. X-ray crystallography of the MDLs revealed high structural similarity between MDL and MIF homotrimers and suggested a potential explanation for the lack of tautomerase activity in the MDLs. MDL1 and MDL2 interacted with each other and with MIF in vitro, in yeast, and in plant leaves and formed hetero-oligomeric complexes with MIF in vitro. The MDLs stimulated signaling through the MIF receptors CXCR2 or CXCR4 and enhanced the responses to MIF in a yeast reporter system, in human neutrophils, and in human lung epithelial cells. Pharmacological inhibitors that disrupted MIF activity or prevented the formation of MIF-MDL hetero-oligomers blocked the observed synergism. These findings demonstrate that MDLs can enhance cellular responses to MIF, which may have functional implications in tissues exposed to MDLs from the diet or environment.


  • Organizational Affiliation

    Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06510, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MIF/D-DT-like protein-1
A, B, C
109Arabidopsis thalianaMutation(s): 0 
Gene Names: MUL3.12MUL3_12At5g57170At5g57170/MUL3_12
UniProt
Find proteins for Q9LU69 (Arabidopsis thaliana)
Explore Q9LU69 
Go to UniProtKB:  Q9LU69
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LU69
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.737α = 90
b = 66.737β = 90
c = 132.32γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection
  • Version 1.2: 2024-07-03
    Changes: Database references