9LNT | pdb_00009lnt

Crystal structure of de novo designed amantadine induced homotrimer mAIT03

• PDB DOI: https://doi.org/10.2210/pdb9LNT/pdb

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


• Deposited: 2025-01-22 Released: 2025-12-17 
• Deposition Author(s): Qihan, J., Longxing, C.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.291 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.238 (DCC) 

Starting Model: in silico

Literature

De novo design of small molecule-regulated protein oligomers.

Jin, Q., Wang, Y., Chen, D., Liao, J., Cui, Z., Fan, Y., Zeng, A., Xie, M., Cao, L.

(2026) Science 391

• PubMed: 41477902 
• DOI: https://doi.org/10.1126/science.ady6017
• Primary Citation of Related Structures:  
  9LNS, 9LNT, 9LP2, 9LYS


• PubMed Abstract: 
  

  Small molecule-regulated protein oligomerization provides a powerful mechanism for manipulating biological processes by controlling protein proximity with high temporal precision. However, such systems only rarely exist in nature and remain a substantial challenge for de novo design. In this work, we describe a computational method for designing protein homooligomers whose assembly is regulated by small-molecule ligands with matching symmetry. We designed protein homotrimers regulated by the Food and Drug Administration (FDA)-approved drug amantadine and further designed amantadine-responsive heterodimers and heterotrimers. Biophysical characterization confirmed their amantadine-dependent assembly, and their crystal structures closely matched the design models. We demonstrated their broad applicability in controlling protein localization, membraneless condensate formation, and gene expression. Our approach opens new avenues for designing small molecule-responsive proteins and expands the chemogenetic toolkit for manipulating complex biological processes.

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Organizational Affiliation: 
• Fudan University, Shanghai, China.
State Key Laboratory of Gene Expression, School of Life Sciences and School of Medicine, Westlake University, Hangzhou, Zhejiang, China.
Artificial Intelligence Drug Design Core Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
School of Engineering, Westlake University, Hangzhou, China.
Center of Synthetic Biology and Integrated Bioengineering, School of Engineering, Westlake University, 600 Dunyu Road, Xihu District, Hangzhou, Zhejiang Province, China.
Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang Province, China.
Key Laboratory of Intelligent Low-Carbon Biosynthesis of Zhejiang Province, Westlake University, Hangzhou, Zhejiang, China.
Affiliated Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, Zhejiang, China.
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 20.37 kDa 
• Atom Count: 1,494 
• Modeled Residue Count: 171 
• Deposited Residue Count: 171 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mAIT03	A, B [auth C], C [auth E]	57	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
308 (Subject of Investigation/LOI)	G [auth C]	(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine C10 H17 N DKNWSYNQZKUICI-CHIWXEEVSA-N
UNX (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], H [auth C]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.291 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.238 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.818	α = 90
b = 58	β = 90
c = 40.818	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Qihan, J., Longxing, C.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFA1303700

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release
  
• Version 1.1: 2026-01-14
  Changes: Database references