8ZXH | pdb_00008zxh

Structure of the red fluorescent protein mScarlet3-H at pH 4.5

• PDB DOI: https://doi.org/10.2210/pdb8ZXH/pdb

• Classification: FLUORESCENT PROTEIN
• Organism(s): Discosoma sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-14 Released: 2025-02-19 
• Deposition Author(s): Li, Y., Zheng, Q., Li, S., Fu, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

A highly stable monomeric red fluorescent protein for advanced microscopy.

Xiong, H., Chang, Q., Ding, J., Wang, S., Zhang, W., Li, Y., Wu, Y., Lin, P., Yang, C., Liu, M., Fang, G., Yang, Y., Xie, J., Qi, D., Jiang, T., Fu, W., Hu, F., Chen, Y., Yue, R., Li, Y., Cui, Y., Li, M., Fan, S., Yang, Y., Xu, Y., Li, D., Zhang, F., Zhao, H., Wu, C., Zheng, Q., Piatkevich, K.D., Fu, Z.

(2025) Nat Methods 22: 1288-1298

• PubMed: 40247125 
• DOI: https://doi.org/10.1038/s41592-025-02676-5
• Primary Citation of Related Structures:  
  8ZXH, 8ZXO


• PubMed Abstract: 
  

  The stability of fluorescent proteins (FPs) is crucial for imaging techniques such as live-cell imaging, super-resolution microscopy and correlative light and electron microscopy. Although stable green and yellow FPs are available, stable monomeric red FPs (RFPs) remain limited. Here we develop an extremely stable monomeric RFP named mScarlet3-H and determine its structure at a 1.5 Å resolution. mScarlet3-H exhibits remarkable resistance to high temperature, chaotropic conditions and oxidative environments, enabling efficient correlative light and electron microscopy imaging and rapid (less than 1 day) whole-organ tissue clearing. In addition, its high photostability allows long-term three-dimensional structured illumination microscopy imaging of mitochondrial dynamics with minimal photobleaching. It also facilitates dual-color live-cell stimulated emission depletion imaging with a high signal-to-noise ratio and strong specificity. Systematic benchmarking against high-performing RFPs established mScarlet3-H as a highly stable RFP for multimodality microscopy in cell cultures and model organisms, complementing green FPs for multiplexed imaging in zebrafish, mice and Nicotiana benthamiana.

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Organizational Affiliation: 
• Key Laboratory of Clinical Laboratory Technology for Precision Medicine, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Public Technology Service Center, Fujian Medical University, Fuzhou, China.
The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
Chinese Institute for Brain Research, Beijing, China.
School of Life Sciences, Westlake University, Hangzhou, China.
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
College of Life Sciences, Zhejiang University, Hangzhou, China.
State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China.
Microscopy core facility of Westlake University, Hangzhou, China.
Institute of Life Sciences, Fuzhou University, Fuzhou, China.
Optofem Technology Company, Beijing, China.
Beijing Nano Insights Technology Co. Ltd, Beijing, China.
National Laboratory of Biomacromolecules, New Cornerstone Science Laboratory, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
Fujian Key Laboratory of Drug Target Discovery and Structural and Functional Research, School of Pharmacy, Fujian Medical University, Fuzhou, China.
School of Pharmacy, Center of Translational Hematology, Fujian Medical University, Fuzhou, China.
State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China.
X-ray crystallography platform of National Protein Science Facility, Tsinghua University, Beijing, China.
Key Laboratory of Clinical Laboratory Technology for Precision Medicine, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Public Technology Service Center, Fujian Medical University, Fuzhou, China. [e-mail].
State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, Xiamen University, Xiamen, China. [e-mail].
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China. [e-mail].
Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China. [e-mail].
College of Life Sciences, Zhejiang University, Hangzhou, China. [e-mail].
Key Laboratory of Clinical Laboratory Technology for Precision Medicine, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Public Technology Service Center, Fujian Medical University, Fuzhou, China. [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: gel filtration

Macromolecule Content 

• Total Structure Weight: 24.81 kDa 
• Atom Count: 1,934 
• Modeled Residue Count: 215 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
red fluorescent protein mYongHong	A	215	Discosoma sp.	Mutation(s): 0
UniProt
Find proteins for Q9U6Y8 (Discosoma sp.) Explore Q9U6Y8  Go to UniProtKB:  Q9U6Y8

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NRQ	A	L-PEPTIDE LINKING	C16 H17 N3 O4 S		MET, TYR, GLY

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.52	α = 90
b = 35.49	β = 109.52
c = 85.66	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Li, Y., Zheng, Q., Li, S., Fu, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32201235
Other government	China	2022J01287

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release
  
• Version 2.0: 2026-03-04
  Changes: Database references, Polymer sequence