6DG6 | pdb_00006dg6

Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic

• PDB DOI: https://doi.org/10.2210/pdb6DG6/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-16 Released: 2019-01-16 
• Deposition Author(s): Jude, K.M., Silva, D.-A., Yu, S., Baker, D., Garcia, K.C.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: in silico

Literature

De novo design of potent and selective mimics of IL-2 and IL-15.

Silva, D.A., Yu, S., Ulge, U.Y., Spangler, J.B., Jude, K.M., Labao-Almeida, C., Ali, L.R., Quijano-Rubio, A., Ruterbusch, M., Leung, I., Biary, T., Crowley, S.J., Marcos, E., Walkey, C.D., Weitzner, B.D., Pardo-Avila, F., Castellanos, J., Carter, L., Stewart, L., Riddell, S.R., Pepper, M., Bernardes, G.J.L., Dougan, M., Garcia, K.C., Baker, D.

(2019) Nature 565: 186-191

• PubMed: 30626941 
• DOI: https://doi.org/10.1038/s41586-018-0830-7
• Primary Citation Related Structures: 
  6DG5, 6DG6


• PubMed Abstract: 
  

  We describe a de novo computational approach for designing proteins that recapitulate the binding sites of natural cytokines, but are otherwise unrelated in topology or amino acid sequence. We use this strategy to design mimics of the central immune cytokine interleukin-2 (IL-2) that bind to the IL-2 receptor βγ _c heterodimer (IL-2Rβγ _c ) but have no binding site for IL-2Rα (also called CD25) or IL-15Rα (also known as CD215). The designs are hyper-stable, bind human and mouse IL-2Rβγ _c with higher affinity than the natural cytokines, and elicit downstream cell signalling independently of IL-2Rα and IL-15Rα. Crystal structures of the optimized design neoleukin-2/15 (Neo-2/15), both alone and in complex with IL-2Rβγ _c , are very similar to the designed model. Neo-2/15 has superior therapeutic activity to IL-2 in mouse models of melanoma and colon cancer, with reduced toxicity and undetectable immunogenicity. Our strategy for building hyper-stable de novo mimetics could be applied generally to signalling proteins, enabling the creation of superior therapeutic candidates.

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Organizational Affiliation: 
• Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Department of Bioengineering, University of Washington, Seattle, WA, USA.
Departments of Biomedical Engineering and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA.
Fred Hutchinson Cancer Research Center, Clinical Research Division, Seattle, WA, USA.
Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Chemistry, University of Cambridge, Cambridge, UK.
Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Howard Hughes Medical Institute, Chevy Chase, MD, USA. [e-mail].
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Howard Hughes Medical Institute, Chevy Chase, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: fluorescence resonance energy transfer

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 72.68 kDa 
• Atom Count: 4,791 
• Modeled Residue Count: 597 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neoleukin-2/15	A, B, C, D, E, F	104	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.226 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/587

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.73	α = 90
b = 86.8	β = 90
c = 92.31	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Jude, K.M., Silva, D.-A., Yu, S., Baker, D., Garcia, K.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	RO1-AI51321

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-01-23
  Changes: Data collection, Database references
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description