9DN6 | pdb_00009dn6

Insulin receptor bound with de novo designed agonist called "RF-405".

• PDB DOI: https://doi.org/10.2210/pdb9DN6/pdb
• EM Map EMD-47031: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2024-09-16 Released: 2025-10-01 
• Deposition Author(s): Bai, X.C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Tuning insulin receptor signaling using de novo-designed agonists.

Wang, X., Cardoso, S., Cai, K., Venkatesh, P., Hung, A., Ng, M., Hall, C., Coventry, B., Lee, D.S., Chowhan, R., Gerben, S., Li, J., An, W., Hon, M., Gao, M., Liao, Y.C., Accili, D., Choi, E., Bai, X.C., Baker, D.

(2025) Mol Cell 85: 4064

• PubMed: 41086805 
• DOI: https://doi.org/10.1016/j.molcel.2025.09.020
• Primary Citation of Related Structures:  
  9DN6, 9DNI, 9DNN


• PubMed Abstract: 
  

  Insulin binding induces conformational changes in the insulin receptor (IR) that activate the intracellular kinase domain and the protein kinase B (AKT) and mitogen-activated protein kinase (MAPK) pathways, regulating metabolism and proliferation. We reasoned that designed agonists inducing different IR conformational changes might induce different downstream responses. We used de novo protein design to generate binders for individual IR extracellular domains and fused them in different orientations with different conformational flexibility. We obtained a series of synthetic IR agonists that elicit a wide range of receptor autophosphorylation, MAPK activation, trafficking, and proliferation responses. We identified designs more potent than insulin, causing longer-lasting glucose lowering in vivo and retaining activity on disease-causing IR mutants, while largely avoiding the cancer cell proliferation induced by insulin. Our findings shed light on how changes in IR conformation and dynamics translate into downstream signaling, and with further development, our synthetic agonists could have therapeutic utility for metabolic and proliferative diseases.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA, USA. Electronic address: [e-mail].
Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA, USA; Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
Department of Biochemistry and Molecular Biophysics, The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.
Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA.
Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA. Electronic address: [e-mail].
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA. Electronic address: [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA; Institute for Protein Design, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 341.24 kDa 
• Atom Count: 14,338 
• Modeled Residue Count: 1,766 
• Deposited Residue Count: 3,000 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
De novo designed IR agonist RF-405	A, B	130	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Short of Insulin receptor	C, D	1,370	Homo sapiens	Mutation(s): 0  Gene Names: INSR EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06213 (Homo sapiens) Explore P06213  Go to UniProtKB:  P06213
PHAROS:  P06213 GTEx:  ENSG00000171105

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Bai, X.C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release
  
• Version 1.1: 2025-10-29
  Changes: Data collection, Database references
• Version 1.2: 2025-11-19
  Changes: Data collection, Database references