9YS3 | pdb_00009ys3

Pr-pr homodimer state of Stigmatella aurantiaca bacteriophytochrome 2

• PDB DOI: https://doi.org/10.2210/pdb9YS3/pdb
• EM Map EMD-73380: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Allostigmatella aurantiaca
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-10-17 Released: 2026-06-17 
• Deposition Author(s): Karki, P., Stojkovic, E.A., Schmidt, M.
• Funding Organization(s): National Science Foundation (NSF, United States), Simons Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.85 Å
• Aggregation State: CELL 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A bacteriophytochrome Pr/Pfr heterodimer studied through single-particle time-resolved cryo-electron microscopy.

Karki, P., Budell, W.C., Kannachel, R., Menendez, D., Hernandez, C., Mendez, J.H., Kanou, S., Singh, M., Slavov, C., Schwander, P., Malla, T.N., Stojkovic, E.A., Schmidt, M.

(2026) Commun Chem 

• PubMed: 42260277 
• DOI: https://doi.org/10.1038/s42004-026-02084-6
• Primary Citation Related Structures: 
  9YS3, 9YXN


• PubMed Abstract: 
  

  Phytochromes are dimeric photoreceptors found in bacteria, fungi, and plants that reversibly interconvert between a red-absorbing Pr state and a far-red-absorbing Pfr state. In bacteria, phytochromes (BphPs) regulate diverse responses through a two-component signaling pathway comprising a C-terminal histidine kinase (HK) and a response regulator. A previous cryo-EM study of the wild-type BphP from Stigmatella aurantiaca (SaBphP2) revealed a stable Pr/Pfr heterodimer in which the two protomers adopt distinct Pr and Pfr conformations. Here, using the Spotiton technique, we captured the same heterodimer by illuminating SaBphP2 particles on the cryo-EM grid and vitrifying them 10 ms later. Comparison with the Pr/Pr homodimer reveals a 180° rotation of the HK domain, driven by an unwinding of the coiled-coil helices that connect the photosensory core to the enzymatic domain. The large-scale reorientations provide mechanistic insight into light-triggered signal transduction mediated by bacterial phytochromes.

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Organizational Affiliation: 
• Department of Physics and Astronomy, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
New York Structural Biology Center, New York, NY, USA.
Department of Biology, Northeastern Illinois University, Chicago, IL, USA.
Department of Chemistry, University of South Florida, Tampa, FL, USA.
Vaccine Research Center Electron Microscopy Unit, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Department of Biology, Northeastern Illinois University, Chicago, IL, USA. [e-mail].
Department of Physics and Astronomy, University of Wisconsin-Milwaukee, Milwaukee, WI, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 161.66 kDa 
• Atom Count: 10,166 
• Modeled Residue Count: 1,478 
• Deposited Residue Count: 1,478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriophytochrome	A, B	739	Allostigmatella aurantiaca	Mutation(s): 0  Gene Names: SAMN05444354_11920 EC: 2.7.13.3
UniProt
Find proteins for A0A1H7ZJA8 (Stigmatella aurantiaca) Explore A0A1H7ZJA8  Go to UniProtKB:  A0A1H7ZJA8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLA (Subject of Investigation/LOI)	C [auth A], D [auth B]	BILIVERDINE IX ALPHA C33 H34 N4 O6 GWZYPXHJIZCRAJ-SRVCBVSDSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.85 Å
• Aggregation State: CELL 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	v4.7.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-17 
Deposition Author(s): Karki, P., Stojkovic, E.A., Schmidt, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--
Simons Foundation	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2026-06-17
  Type: Initial release
  
• Version 1.1: 2026-06-24
  Changes: Data collection, Database references