3QAZ

IL-2 mutant D10 ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.292 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1038/nature10975
  • Primary Citation of Related Structures:  
    3QAZ, 3QB1

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-2136Homo sapiensMutation(s): 6 
Gene Names: IL2
UniProt & NIH Common Fund Data Resources
Find proteins for P60568 (Homo sapiens)
Explore P60568 
Go to UniProtKB:  P60568
GTEx:  ENSG00000109471 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60568
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-2 receptor subunit beta217Homo sapiensMutation(s): 5 
Gene Names: IL2RB
UniProt & NIH Common Fund Data Resources
Find proteins for P14784 (Homo sapiens)
Explore P14784 
Go to UniProtKB:  P14784
GTEx:  ENSG00000100385 
Entity Groups  
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UniProt GroupP14784
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytokine receptor common subunit gamma202Homo sapiensMutation(s): 1 
Gene Names: IL2RG
UniProt & NIH Common Fund Data Resources
Find proteins for P31785 (Homo sapiens)
Explore P31785 
Go to UniProtKB:  P31785
GTEx:  ENSG00000147168 
Entity Groups  
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UniProt GroupP31785
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AB [auth I]
AC [auth Z]
BB [auth I]
BC [auth a]
CB [auth K]
AB [auth I],
AC [auth Z],
BB [auth I],
BC [auth a],
CB [auth K],
CC [auth a],
DB [auth K],
DC [auth c],
EB [auth L],
EC [auth c],
FB [auth L],
FC [auth d],
GB [auth L],
GC [auth f],
HB [auth L],
HC [auth g],
IB [auth N],
IC [auth g],
JB [auth O],
JC [auth i],
KA [auth B],
KB [auth O],
KC [auth i],
LA [auth C],
LB [auth O],
LC [auth j],
MA [auth C],
MB [auth O],
NA [auth C],
NB [auth O],
OA [auth C],
OB [auth Q],
PA [auth C],
PB [auth R],
QA [auth E],
QB [auth R],
RA [auth F],
RB [auth R],
SA [auth F],
SB [auth R],
TA [auth F],
TB [auth R],
UA [auth F],
UB [auth T],
VA [auth F],
VB [auth U],
WA [auth H],
WB [auth U],
XA [auth I],
XB [auth W],
YA [auth I],
YB [auth X],
ZA [auth I],
ZB [auth X]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.291 
  • R-Value Observed: 0.292 
  • 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
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-11
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Structure summary
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary