Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 62.47 kDa 
• Atom Count: 4100 
• Modelled Residue Count: 492 
• Deposited Residue Count: 512 
• Unique protein chains: 3

6DG5

Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic complex with IL-2Rb and IL-2Rg

• PDB DOI: 10.2210/pdb6DG5/pdb

• Classification: BIOSYNTHETIC PROTEIN/Protein Binding
• Organism(s): synthetic construct, Mus musculus
• Expression System: Escherichia coli, Trichoplusia ni
• 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: 2.52 Å
• R-Value Free: 0.266 
• R-Value Work: 0.221 
• R-Value Observed: 0.226 

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: 10.1038/s41586-018-0830-7
• Primary Citation of 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: 

Howard Hughes Medical Institute, Chevy Chase, MD, USA. [e-mail].

Macromolecules

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-2 receptor subunit beta	B	209	Mus musculus	Mutation(s): 0  Gene Names: Il2rb
UniProt & NIH Common Fund Data Resources
Find proteins for P16297 (Mus musculus) Explore P16297  Go to UniProtKB:  P16297
IMPC:  MGI:96550

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytokine receptor common subunit gamma	C	199	Mus musculus	Mutation(s): 0  Gene Names: Il2rg
UniProt
Find proteins for P34902 (Mus musculus) Explore P34902  Go to UniProtKB:  P34902

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	E	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G27389SR GlyCosmos:  G27389SR GlyGen:  G27389SR

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth C], G [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.266 
• R-Value Work: 0.221 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2 2₁
• Diffraction Data DOI: 10.15785/SBGRID/588 SBGrid

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.125	α = 90
b = 67.914	β = 90
c = 172.084	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-05-16 
• 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, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary