4GS7

Structure of the Interleukin-15 quaternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report



Literature

Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15.

Ring, A.M.Lin, J.X.Feng, D.Mitra, S.Rickert, M.Bowman, G.R.Pande, V.S.Li, P.Moraga, I.Spolski, R.Ozkan, E.Leonard, W.J.Garcia, K.C.

(2012) Nat Immunol 13: 1187-1195

  • DOI: 10.1038/ni.2449
  • Primary Citation of Related Structures:  
    4GS7

  • PubMed Abstract: 
  • Interleukin 15 (IL-15) and IL-2 have distinct immunological functions even though both signal through the receptor subunit IL-2Rβ and the common γ-chain (γ(c)). Here we found that in the structure of the IL-15-IL-15Rα-IL-2Rβ-γ(c) quaternary complex, ...

    Interleukin 15 (IL-15) and IL-2 have distinct immunological functions even though both signal through the receptor subunit IL-2Rβ and the common γ-chain (γ(c)). Here we found that in the structure of the IL-15-IL-15Rα-IL-2Rβ-γ(c) quaternary complex, IL-15 binds to IL-2Rβ and γ(c) in a heterodimer nearly indistinguishable from that of the IL-2-IL-2Rα-IL-2Rβ-γ(c) complex, despite their different receptor-binding chemistries. IL-15Rα substantially increased the affinity of IL-15 for IL-2Rβ, and this allostery was required for IL-15 trans signaling. Consistent with their identical IL-2Rβ-γ(c) dimer geometries, IL-2 and IL-15 showed similar signaling properties in lymphocytes, with any differences resulting from disparate receptor affinities. Thus, IL-15 and IL-2 induced similar signals, and the cytokine specificity of IL-2Rα versus IL-15Rα determined cellular responsiveness. Our results provide new insights for the development of specific immunotherapeutics based on IL-15 or IL-2.


    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-15A116Homo sapiensMutation(s): 0 
Gene Names: IL15
Find proteins for P40933 (Homo sapiens)
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Go to UniProtKB:  P40933
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PHAROS  P40933
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-2 receptor subunit betaB217Homo sapiensMutation(s): 3 
Gene Names: IL2RBIL15RB
Find proteins for P14784 (Homo sapiens)
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PHAROS  P14784
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytokine receptor common subunit gammaC203Homo sapiensMutation(s): 1 
Gene Names: IL2RG
Find proteins for P31785 (Homo sapiens)
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PHAROS  P31785
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-15 receptor subunit alphaD69Homo sapiensMutation(s): 0 
Gene Names: IL15RA
Find proteins for Q13261 (Homo sapiens)
Explore Q13261 
Go to UniProtKB:  Q13261
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PHAROS  Q13261
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
AL-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.949α = 90
b = 74.61β = 90
c = 129.211γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2012-11-14
    Changes: Database references
  • Version 1.2: 2012-12-05
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary