5UWC | pdb_00005uwc

Cytokine-receptor complex

• PDB DOI: https://doi.org/10.2210/pdb5UWC/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-02-21 Released: 2018-02-07 
• Deposition Author(s): Broughton, S.E., Parker, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.242 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Models: experimental

Literature

A dual role for the N-terminal domain of the IL-3 receptor in cell signalling.

Broughton, S.E., Hercus, T.R., Nero, T.L., Kan, W.L., Barry, E.F., Dottore, M., Cheung Tung Shing, K.S., Morton, C.J., Dhagat, U., Hardy, M.P., Wilson, N.J., Downton, M.T., Schieber, C., Hughes, T.P., Lopez, A.F., Parker, M.W.

(2018) Nat Commun 9: 386-386

• PubMed: 29374162 
• DOI: https://doi.org/10.1038/s41467-017-02633-7
• Primary Citation Related Structures: 
  5UV8, 5UWC


• PubMed Abstract: 
  

  The interleukin-3 (IL-3) receptor is a cell-surface heterodimer that links the haemopoietic, vascular and immune systems and is overexpressed in acute and chronic myeloid leukaemia progenitor cells. It belongs to the type I cytokine receptor family in which the α-subunits consist of two fibronectin III-like domains that bind cytokine, and a third, evolutionarily unrelated and topologically conserved, N-terminal domain (NTD) with unknown function. Here we show by crystallography that, while the NTD of IL3Rα is highly mobile in the presence of IL-3, it becomes surprisingly rigid in the presence of IL-3 K116W. Mutagenesis, biochemical and functional studies show that the NTD of IL3Rα regulates IL-3 binding and signalling and reveal an unexpected role in preventing spontaneous receptor dimerisation. Our work identifies a dual role for the NTD in this cytokine receptor family, protecting against inappropriate signalling and dynamically regulating cytokine receptor binding and function.

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Organizational Affiliation: 
• Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia.
The Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, 5000, Australia.
Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
CSL Limited, Parkville, VIC, 3010, Australia.
IBM Research Australia, Level 5, 204 Lygon Street, Carlton, VIC, 3053, Australia.
South Australian Health and Medical Research Institute and University of Adelaide, Adelaide, SA, 5000, Australia.
The Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, 5000, Australia. [e-mail].
Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia. [e-mail].
Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.76 kDa 
• Atom Count: 3,125 
• Modeled Residue Count: 365 
• Deposited Residue Count: 410 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-3 receptor subunit alpha	A [auth G]	288	Homo sapiens	Mutation(s): 2  Gene Names: IL3RA, IL3R
UniProt & NIH Common Fund Data Resources
Find proteins for P26951 (Homo sapiens) Explore P26951  Go to UniProtKB:  P26951
PHAROS:  P26951 GTEx:  ENSG00000185291

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-3	B [auth I]	122	Homo sapiens	Mutation(s): 2  Gene Names: IL3
UniProt & NIH Common Fund Data Resources
Find proteins for P08700 (Homo sapiens) Explore P08700  Go to UniProtKB:  P08700
PHAROS:  P08700 GTEx:  ENSG00000164399

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth A]	3		N/A
Glycosylation Resources
GlyTouCan: G28454KX GlyCosmos: G28454KX GlyGen: G28454KX

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDT	G	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID C10 H16 N2 O8 KCXVZYZYPLLWCC-UHFFFAOYSA-N
NAG	D [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CIT	E [auth G], H [auth I]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
IMD	F [auth G]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.242 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.461	α = 90
b = 106.461	β = 90
c = 96.116	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): Broughton, S.E., Parker, M.W.

Revision History  

• Version 1.0: 2018-02-07
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary