3QAZ

IL-2 mutant D10 ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.802 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.291 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'

Levin, A.M.Bates, D.L.Ring, A.M.Krieg, C.Lin, J.T.Su, L.Moraga, I.Raeber, M.E.Bowman, G.R.Novick, P.Pande, V.S.Fathman, C.G.Boyman, O.Garcia, K.C.

(2012) Nature 484: 529-533

  • DOI: 10.1038/nature10975
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The immunostimulatory cytokine interleukin-2 (IL-2) is a growth factor for a wide range of leukocytes, including T cells and natural killer (NK) cells. Considerable effort has been invested in using IL-2 as a therapeutic agent for a variety of immune ...

    The immunostimulatory cytokine interleukin-2 (IL-2) is a growth factor for a wide range of leukocytes, including T cells and natural killer (NK) cells. Considerable effort has been invested in using IL-2 as a therapeutic agent for a variety of immune disorders ranging from AIDS to cancer. However, adverse effects have limited its use in the clinic. On activated T cells, IL-2 signals through a quaternary 'high affinity' receptor complex consisting of IL-2, IL-2Rα (termed CD25), IL-2Rβ and IL-2Rγ. Naive T cells express only a low density of IL-2Rβ and IL-2Rγ, and are therefore relatively insensitive to IL-2, but acquire sensitivity after CD25 expression, which captures the cytokine and presents it to IL-2Rβ and IL-2Rγ. Here, using in vitro evolution, we eliminated the functional requirement of IL-2 for CD25 expression by engineering an IL-2 'superkine' (also called super-2) with increased binding affinity for IL-2Rβ. Crystal structures of the IL-2 superkine in free and receptor-bound forms showed that the evolved mutations are principally in the core of the cytokine, and molecular dynamics simulations indicated that the evolved mutations stabilized IL-2, reducing the flexibility of a helix in the IL-2Rβ binding site, into an optimized receptor-binding conformation resembling that when bound to CD25. The evolved mutations in the IL-2 superkine recapitulated the functional role of CD25 by eliciting potent phosphorylation of STAT5 and vigorous proliferation of T cells irrespective of CD25 expression. Compared to IL-2, the IL-2 superkine induced superior expansion of cytotoxic T cells, leading to improved antitumour responses in vivo, and elicited proportionally less expansion of T regulatory cells and reduced pulmonary oedema. Collectively, we show that in vitro evolution has mimicked the functional role of CD25 in enhancing IL-2 potency and regulating target cell specificity, which has implications for immunotherapy.


    Organizational Affiliation

    Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Interleukin-2
A, D, G, J, M, P, S, V, Y, b, e, h
136Homo sapiensMutation(s): 6 
Gene Names: IL2
Find proteins for P60568 (Homo sapiens)
Go to Gene View: IL2
Go to UniProtKB:  P60568
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Interleukin-2 receptor subunit beta
B, E, H, K, N, Q, T, W, Z, c, f, i
217Homo sapiensMutation(s): 5 
Gene Names: IL2RB (IL15RB)
Find proteins for P14784 (Homo sapiens)
Go to Gene View: IL2RB
Go to UniProtKB:  P14784
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Cytokine receptor common subunit gamma
C, F, I, L, O, R, U, X, a, d, g, j
202Homo sapiensMutation(s): 1 
Gene Names: IL2RG
Find proteins for P31785 (Homo sapiens)
Go to Gene View: IL2RG
Go to UniProtKB:  P31785
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
a, B, C, c, d, E, f, F, g, H, i, I, j, K, L, N, O, Q, R, T, U, W, X, Z
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.802 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.291 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 118.226α = 99.86
b = 118.099β = 99.86
c = 236.115γ = 99.74
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2014-10-15
    Type: Structure summary