9DD1 | pdb_00009dd1

Designed allosteric facilitated dissociation switch AS1 in complex state THE with methylated lysines

• PDB DOI: https://doi.org/10.2210/pdb9DD1/pdb

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


• Deposited: 2024-08-27 Released: 2025-08-20 
• Deposition Author(s): Bera, A.K., Broerman, A., Baker, D.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free: 
  0.277 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: in silico

Literature

Design of facilitated dissociation enables timing of cytokine signalling.

Broerman, A.J., Pollmann, C., Zhao, Y., Lichtenstein, M.A., Jackson, M.D., Tessmer, M.H., Ryu, W.H., Ogishi, M., Abedi, M.H., Sahtoe, D.D., Allen, A., Kang, A., De La Cruz, J., Brackenbrough, E., Sankaran, B., Bera, A.K., Zuckerman, D.M., Stoll, S., Garcia, K.C., Praetorius, F., Piehler, J., Baker, D.

(2025) Nature 

• PubMed: 40993395 
• DOI: https://doi.org/10.1038/s41586-025-09549-z
• Primary Citation of Related Structures:  
  9DCX, 9DCY, 9DCZ, 9DD0, 9DD1, 9DD2, 9DD3, 9DD4, 9DD5, 9OLQ


• PubMed Abstract: 
  

  Protein design has focused on the design of ground states, ensuring that they are sufficiently low energy to be highly populated ¹ . Designing the kinetics and dynamics of a system requires, in addition, the design of excited states that are traversed in transitions from one low-lying state to another ^2,3 . This is a challenging task because such states must be sufficiently strained to be poorly populated, but not so strained that they are not populated at all, and because protein design methods have focused on generating near-ideal structures ^4-7 . Here we describe a general approach for designing systems that use an induced-fit power stroke ⁸ to generate a structurally frustrated ⁹ and strained excited state, allosterically driving protein complex dissociation. X-ray crystallography, double electron-electron resonance spectroscopy and kinetic binding measurements show that incorporating excited states enables the design of effector-induced increases in dissociation rates as high as 5,700-fold. We highlight the power of this approach by designing rapid biosensors, kinetically controlled circuits and cytokine mimics that can be dissociated from their receptors within seconds, enabling dissection of the temporal dynamics of interleukin-2 signalling.

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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].
Department of Chemical Engineering, University of Washington, Seattle, WA, USA. [e-mail].
Department of Biology/Chemistry, Osnabrück University, Osnabrück, Germany.
Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany.
Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
Department of Chemistry, University of Washington, Seattle, WA, USA.
Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.
Department of Biochemistry, University of Washington, Seattle, WA, USA.
Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA. [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA, USA. [e-mail].
Institute of Science and Technology Austria, Klosterneuburg, Austria. [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, University of Washington, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 45.82 kDa 
• Atom Count: 3,062 
• Modeled Residue Count: 390 
• Deposited Residue Count: 404 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed allosteric facilitated dissociation switch AS1 T	A	258	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed allosteric facilitated dissociation switch AS1 E	B	24	synthetic construct	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed allosteric facilitated dissociation switch AS1 H	C	122	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.70 Å
• R-Value Free:  0.277 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.859	α = 90
b = 110.859	β = 90
c = 65.532	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Bera, A.K., Broerman, A., Baker, D.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release
  
• Version 1.1: 2025-09-24
  Changes: Database references
• Version 1.2: 2025-10-08
  Changes: Database references