9LQM | pdb_00009lqm

Crystal structure of synthetic ubiquitin variant R4 designed by ProteinMPNN

• PDB DOI: https://doi.org/10.2210/pdb9LQM/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-28 Released: 2025-02-12 
• Deposition Author(s): Lu, W.-L., Ko, T.-P., Wu, K.-P.
• Funding Organization(s): Academia Sinica (Taiwan), Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Mesostructured Water Enhances Stability of ProteinMPNN-Designed Ubiquitin-Fold Proteins.

Chen, L.Y., Lu, W.L., Pathania, T., Chu, I.H., Ho, M.R., Chuang, W.C., Lou, Y.C., Hung, T.I., Miyanoiri, Y., Chang, C.A., Wu, K.P.

(2026) J Am Chem Soc 

• PubMed: 41643123 
• DOI: https://doi.org/10.1021/jacs.5c19875
• Primary Citation of Related Structures:  
  9LQK, 9LQM, 9M8W, 9M8X, 9M9G, 9M9H


• PubMed Abstract: 
  

  AI-designed protein variants have demonstrated remarkable resistance to heat and chemical stress, yet the molecular mechanisms underlying this stability remain unclear. Here, we present a comprehensive biophysical and nuclear magnetic resonance (NMR) analysis of thermally stable ubiquitin and its ProteinMPNN-designed variants, R4 and R10, together with a second system based on the less stable ISG15 C-terminal domain (ISG15-CTD). Both R4/R10 and ProteinMPNN-designed ISG15-CTD variants (ICVs) exhibit extraordinary thermostability beyond 120 °C, and resist extreme denaturation at pH 3.0 in 8 M urea. NMR relaxation and hydrogen-deuterium exchange, and molecular-dynamics simulations reveal a protective mesostructured hydration shell that strengthens the hydrogen bonding network between protein-bound and bulk water, thereby suppressing unfolding. Sequence and electrostatic analyses indicate that this hydration arises from charge enrichment and clustering on the protein surface. These findings identify mesostructured hydration as a general, sequence-encoded mechanism of ProteinMPNN-driven stability and provide a physical framework for designing highly resilient biomolecules.

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Organizational Affiliation: 
• Institute of Biological Chemistry, Academia Sinica, Taipei 115201, Taiwan.
Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 106319, Taiwan.
Department of Chemistry, University of California Riverside, Riverside, California 92521, United States.
Biomedical Translation Research Center, Academia Sinica, Taipei 115201, Taiwan.
Research Center for Next-Generation Protein Sciences, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.91 kDa 
• Atom Count: 1,540 
• Modeled Residue Count: 161 
• Deposited Residue Count: 206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin variant R4	A, B	103	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.196 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.845	α = 90
b = 50.845	β = 90
c = 102.666	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Lu, W.-L., Ko, T.-P., Wu, K.-P.

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Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	AS-GCS-113-L05
Academia Sinica (Taiwan)	Taiwan	AS-CDA-110-L03
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	NSTC-113-2113-M-001-030

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release
  
• Version 1.1: 2026-02-18
  Changes: Database references