3DI3

Crystal structure of the complex of human interleukin-7 with glycosylated human interleukin-7 receptor alpha ectodomain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

wwPDB Validation 3D Report Full Report



Literature

Structural and Biophysical Studies of the Human IL-7/IL-7Ralpha Complex.

McElroy, C.A.Dohm, J.A.Walsh, S.T.

(2009) Structure 17: 54-65

  • DOI: 10.1016/j.str.2008.10.019
  • Primary Citation of Related Structures:  
    3DI2, 3DI3

  • PubMed Abstract: 
  • IL-7 and IL-7Ralpha bind the gamma(c) receptor, forming a complex crucial to several signaling cascades leading to the development and homeostasis of T and B cells. We report that the IL-7Ralpha ectodomain uses glycosylation to modulate its binding c ...

    IL-7 and IL-7Ralpha bind the gamma(c) receptor, forming a complex crucial to several signaling cascades leading to the development and homeostasis of T and B cells. We report that the IL-7Ralpha ectodomain uses glycosylation to modulate its binding constants to IL-7, unlike the other receptors in the gamma(c) family. IL-7 binds glycosylated IL-7Ralpha 300-fold more tightly than unglycosylated IL-7Ralpha, and the enhanced affinity is attributed primarily to an accelerated on rate. Structural comparison of IL-7 in complex to both forms of IL-7Ralpha reveals that glycosylation does not participate directly in the binding interface. The SCID mutations of IL-7Ralpha locate outside the binding interface with IL-7, suggesting that the expressed mutations cause protein folding defects in IL-7Ralpha. The IL-7/IL-7Ralpha structures provide a window into the molecular recognition events of the IL-7 signaling cascade and provide sites to target for designing new therapeutics to treat IL-7-related diseases.


    Organizational Affiliation

    Department of Molecular and Cellular Biochemistry, College of Medicine, Comprehensive Cancer Center, Ohio State University, 467 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-7A154Homo sapiensMutation(s): 1 
Gene Names: IL7
Find proteins for P13232 (Homo sapiens)
Explore P13232 
Go to UniProtKB:  P13232
NIH Common Fund Data Resources
PHAROS  P13232
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Interleukin-7 receptor subunit alphaB223Homo sapiensMutation(s): 1 
Gene Names: IL7R
Find proteins for P16871 (Homo sapiens)
Explore P16871 
Go to UniProtKB:  P16871
NIH Common Fund Data Resources
PHAROS  P16871
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E
2 N-Glycosylation
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.573α = 90
b = 68.235β = 90
c = 112.273γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary