Crystal structure of the unliganded human interleukin-7 receptor extracellular domain

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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Structural reorganization of the interleukin-7 signaling complex.

McElroy, C.A.Holland, P.J.Zhao, P.Lim, J.M.Wells, L.Eisenstein, E.Walsh, S.T.

(2012) Proc Natl Acad Sci U S A 109: 2503-2508

  • DOI: https://doi.org/10.1073/pnas.1116582109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We report here an unliganded receptor structure in the common gamma-chain (γ(c)) family of receptors and cytokines. The crystal structure of the unliganded form of the interleukin-7 alpha receptor (IL-7Rα) extracellular domain (ECD) at 2.15 Å resolution reveals a homodimer forming an "X" geometry looking down onto the cell surface with the C termini of the two chains separated by 110 Å and the dimer interface comprising residues critical for IL-7 binding. Further biophysical studies indicate a weak association of the IL-7Rα ECDs but a stronger association between the γ(c)/IL-7Rα ECDs, similar to previous studies of the full-length receptors on CD4(+) T cells. Based on these and previous results, we propose a molecular mechanism detailing the progression from the inactive IL-7Rα homodimer and IL-7Rα-γ(c) heterodimer to the active IL-7-IL-7Rα-γ(c) ternary complex whereby the two receptors undergo at least a 90° rotation away from the cell surface, moving the C termini of IL-7Rα and γ(c) from a distance of 110 Å to less than 30 Å at the cell surface. This molecular mechanism can be used to explain recently discovered IL-7- and γ(c)-independent gain-of-function mutations in IL-7Rα from B- and T-cell acute lymphoblastic leukemia patients. The mechanism may also be applicable to other γ(c) receptors that form inactive homodimers and heterodimers independent of their cytokines.

  • Organizational Affiliation

    Battelle Biomedical Research Center, Columbus, OH 43201, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interleukin-7 receptor subunit alpha
A, B
223Homo sapiensMutation(s): 1 
Gene Names: IL7R
UniProt & NIH Common Fund Data Resources
Find proteins for P16871 (Homo sapiens)
Explore P16871 
Go to UniProtKB:  P16871
PHAROS:  P16871
GTEx:  ENSG00000168685 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16871
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NGA

Download Ideal Coordinates CCD File 
J [auth B]2-acetamido-2-deoxy-beta-D-galactopyranose
C8 H15 N O6
Query on FUC

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
C6 H12 O5
Query on SO4

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F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B]
O4 S
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B],
O [auth B],
P [auth B]
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.424α = 90
b = 101.259β = 90
c = 151.994γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-08-22
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2022-12-21
    Changes: Database references, Structure summary