8R45 | pdb_00008r45

Phytochromobilin-adducted PAS-GAF bidomain of Glycine max phytochrome A

• PDB DOI: https://doi.org/10.2210/pdb8R45/pdb

• Classification: PLANT PROTEIN
• Organism(s): Glycine max
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-11-13 Released: 2025-01-08 
• Deposition Author(s): Guan, K., Chen, P., Nagano, S., Hughes, J.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.192 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

Pr and Pfr structures of plant phytochrome A.

Nagano, S., von Stetten, D., Guan, K., Chen, P.Y., Song, C., Barends, T., Weiss, M.S., Feiler, C.G., Dorner, K., de Diego Martinez, I., Schubert, R., Bielecki, J., Brings, L., Han, H., Kharitonov, K., Kim, C., Kloos, M., Koliyadu, J.C.P., Koua, F.H.M., Round, E., Sarma, A., Sato, T., Schmidt, C., Valerio, J., Wrona, A., Schulz, J., de Wijn, R., Letrun, R., Bean, R., Mancuso, A., Heyne, K., Hughes, J.

(2025) Nat Commun 16: 5319-5319

• PubMed: 40544164 
• DOI: https://doi.org/10.1038/s41467-025-60738-w
• Primary Citation Related Structures: 
  8R44, 8R45, 9ER4, 9F4I, 9QZT


• PubMed Abstract: 
  

  Phytochromes are biliprotein photoreceptors widespread amongst microorganisms and ubiquitous in plants where they control developmental processes as diverse as germination, stem elongation and floral induction through the photoconversion of inactive Pr to the Pfr signalling state. Here we report crystal structures of the chromophore-binding module of soybean phytochrome A, including ~2.2 Å XFEL structures of Pr and Pfr at ambient temperature and high resolution cryogenic structures of Pr. In the Pfr structure, the chromophore is exposed to the medium, the D-ring remaining α-facial following the likely clockwise photoflip. The chromophore shifts within its pocket, while its propionate side chains, their partners as well as three neighbouring tyrosines shift radically. Helices near the chromophore show substantial shifts that might represent components of the light signal. These changes reflect those in bacteriophytochromes despite their quite different signalling mechanisms, implying that fundamental aspects of phytochrome photoactivation have been repurposed for photoregulation in the eukaryotic plant.

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Organizational Affiliation: 
• Institute for Plant Physiology, Justus Liebig University, Giessen, Germany.
Department of Physics, Free University of Berlin, Berlin, Germany.
Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany.
European Molecular Biology Laboratory (EMBL), Hamburg, Germany.
Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.
Department of Analytical Chemistry, University of Leipzig, Leipzig, Germany.
Helmholtz-Zentrum Berlin für Materialien und Energie, BESSY II, Macromolecular Crystallography, Berlin, Germany.
European XFEL GmbH, Schenefeld, Germany.
Diamond light source, Didcot, United Kingdom.
Institute for Plant Physiology, Justus Liebig University, Giessen, Germany. [e-mail].
Department of Physics, Free University of Berlin, Berlin, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 81.42 kDa 
• Atom Count: 5,548 
• Modeled Residue Count: 634 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytochrome A-2	A, B	359	Glycine max	Mutation(s): 0  Gene Names: PHYA2, GLYMA_20G090000
UniProt
Find proteins for B4YB07 (Glycine max) Explore B4YB07  Go to UniProtKB:  B4YB07

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O6E (Subject of Investigation/LOI)	C [auth A], E [auth B]	3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid C33 H38 N4 O6 SRFSSETUPHUBBC-GMXXPEQVSA-N
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.192 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.542	α = 90
b = 112.526	β = 92.078
c = 68.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-08 
Deposition Author(s): Guan, K., Chen, P., Nagano, S., Hughes, J.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB1078

Revision History  

• Version 1.0: 2025-01-08
  Type: Initial release
  
• Version 1.1: 2025-02-19
  Changes: Database references
• Version 1.2: 2025-07-02
  Changes: Database references