9HSA | pdb_00009hsa

Solution structure of X55, a computationally designed protein

• PDB DOI: https://doi.org/10.2210/pdb9HSA/pdb

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


• Deposited: 2024-12-19 Released: 2025-04-23 
• Deposition Author(s): Schweimer, K., Hennig, J., Perez-Borrajero, C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

AlphaDesign: a de novo protein design framework based on AlphaFold.

Jendrusch, M.A., Yang, A.L.J., Cacace, E., Bobonis, J., Voogdt, C.G.P., Kaspar, S., Schweimer, K., Perez-Borrajero, C., Lapouge, K., Scheurich, J., Remans, K., Hennig, J., Typas, A., Korbel, J.O., Sadiq, S.K.

(2025) Mol Syst Biol 21: 1166-1189

• PubMed: 40527958 
• DOI: https://doi.org/10.1038/s44320-025-00119-z
• Primary Citation Related Structures: 
  9HSA


• PubMed Abstract: 
  

  De novo protein design is of fundamental interest to synthetic biology, with a plethora of computational methods of various degrees of generality developed in recent years. Here, we introduce AlphaDesign, a hallucination-based computational framework for de novo protein design developed with maximum generality and usability in mind, which combines AlphaFold with autoregressive diffusion models to enable rapid generation and computational validation of proteins with controllable interactions, conformations and oligomeric state without the requirement for class-dependent model re-training or fine-tuning. We apply our framework to design and systematically validate in vivo active inhibitors of a family of bacterial phage defense systems with toxic effectors called retrons, paving the way towards efficient, rational design of novel proteins as biologics.

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Organizational Affiliation: 
• European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany.
Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
Chair of Biochemistry IV, Biophysical Chemistry, University of Bayreuth, 95447, Bayreuth, Germany.
Protein Expression and Purification Core Facility, EMBL, Heidelberg, Germany.
European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. [e-mail].
European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. [e-mail].
DenovAI Biotech Ltd., Rehovot, 7670104, Israel. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 12.04 kDa 
• Atom Count: 850 
• Modeled Residue Count: 102 
• Deposited Residue Count: 102 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
X55	A	102	Escherichia coli	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Schweimer, K., Hennig, J., Perez-Borrajero, C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Database references
• Version 1.2: 2025-09-17
  Changes: Database references