6NCU

Interleukin-37 residues 53-206- dimer

  • Classification: CYTOKINE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-12-12 Released: 2019-03-13 
  • Deposition Author(s): Eisenmesser, E.Z.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.399 
  • R-Value Work: 0.340 
  • R-Value Observed: 0.346 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Interleukin-37 monomer is the active form for reducing innate immunity.

Eisenmesser, E.Z.Gottschlich, A.Redzic, J.S.Paukovich, N.Nix, J.C.Azam, T.Zhang, L.Zhao, R.Kieft, J.S.The, E.Meng, X.Dinarello, C.A.

(2019) Proc Natl Acad Sci U S A 116: 5514-5522

  • DOI: 10.1073/pnas.1819672116
  • Primary Citation of Related Structures:  
    6NCU

  • PubMed Abstract: 
  • Interleukin-37 (IL-37), a member of the IL-1 family of cytokines, is a fundamental suppressor of innate and acquired immunities. Here, we used an integrative approach that combines biophysical, biochemical, and biological studies to elucidate the unique characteristics of IL-37 ...

    Interleukin-37 (IL-37), a member of the IL-1 family of cytokines, is a fundamental suppressor of innate and acquired immunities. Here, we used an integrative approach that combines biophysical, biochemical, and biological studies to elucidate the unique characteristics of IL-37. Our studies reveal that single amino acid mutations at the IL-37 dimer interface that result in the stable formation of IL-37 monomers also remain monomeric at high micromolar concentrations and that these monomeric IL-37 forms comprise higher antiinflammatory activities than native IL-37 on multiple cell types. We find that, because native IL-37 forms dimers with nanomolar affinity, higher IL-37 only weakly suppresses downstream markers of inflammation whereas lower concentrations are more effective. We further show that IL-37 is a heparin binding protein that modulates this self-association and that the IL-37 dimers must block the activity of the IL-37 monomer. Specifically, native IL-37 at 2.5 nM reduces lipopolysaccharide (LPS)-induced vascular cell adhesion molecule (VCAM) protein levels by ∼50%, whereas the monomeric D73K mutant reduced VCAM by 90% at the same concentration. Compared with other members of the IL-1 family, both the N and the C termini of IL-37 are extended, and we show they are disordered in the context of the free protein. Furthermore, the presence of, at least, one of these extended termini is required for IL-37 suppressive activity. Based on these structural and biological studies, we present a model of IL-37 interactions that accounts for its mechanism in suppressing innate inflammation.


    Organizational Affiliation

    Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-37A, B154Homo sapiensMutation(s): 0 
Gene Names: IL37FIL1ZIL1F7IL1H4IL1RP1
Find proteins for Q9NZH6 (Homo sapiens)
Explore Q9NZH6 
Go to UniProtKB:  Q9NZH6
NIH Common Fund Data Resources
PHAROS:  Q9NZH6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.399 
  • R-Value Work: 0.340 
  • R-Value Observed: 0.346 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.51α = 90
b = 67.51β = 90
c = 142.74γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-12-12 
  • Released Date: 2019-03-13 
  • Deposition Author(s): Eisenmesser, E.Z.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR03 CA219743

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-22
    Changes: Author supporting evidence