3UP1 | pdb_00003up1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.257 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

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 Related Structures: 
    3UP1

  • 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.

Macromolecule Content 

  • Total Structure Weight: 53.63 kDa 
  • Atom Count: 3,517 
  • Modeled Residue Count: 397 
  • Deposited Residue Count: 446 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGA

Query on NGA



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

Query on FUC



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B]
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B],
O [auth B],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.257 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
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
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 2.2: 2024-10-30
    Changes: Data collection, Structure summary