4OUR | pdb_00004our

Crystal structure of Arabidopsis thaliana phytochrome B photosensory module

• PDB DOI: https://doi.org/10.2210/pdb4OUR/pdb

• Classification: GENE REGULATION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-02-18 Released: 2014-07-16 
• Deposition Author(s): Sethe Burgie, E., Bussell, A.N., Walker, J.M., Dubiel, K., Vierstra, R.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 
  0.270 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome.

Burgie, E.S., Bussell, A.N., Walker, J.M., Dubiel, K., Vierstra, R.D.

(2014) Proc Natl Acad Sci U S A 111: 10179-10184

• PubMed: 24982198 
• DOI: https://doi.org/10.1073/pnas.1403096111
• Primary Citation Related Structures: 
  4OUR


• PubMed Abstract: 
  

  Many aspects of plant photomorphogenesis are controlled by the phytochrome (Phy) family of bilin-containing photoreceptors that detect red and far-red light by photointerconversion between a dark-adapted Pr state and a photoactivated Pfr state. Whereas 3D models of prokaryotic Phys are available, models of their plant counterparts have remained elusive. Here, we present the crystal structure of the photosensing module (PSM) from a seed plant Phy in the Pr state using the PhyB isoform from Arabidopsis thaliana. The PhyB PSM crystallized as a head-to-head dimer with strong structural homology to its bacterial relatives, including a 5(Z)syn, 10(Z)syn, 15(Z)anti configuration of the phytochromobilin chromophore buried within the cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) domain, and a well-ordered hairpin protruding from the Phy-specific domain toward the bilin pocket. However, its Per/Arnt/Sim (PAS) domain, knot region, and helical spine show distinct structural differences potentially important to signaling. Included is an elongated helical spine, an extended β-sheet connecting the GAF domain and hairpin stem, and unique interactions between the region upstream of the PAS domain knot and the bilin A and B pyrrole rings. Comparisons of this structure with those from bacterial Phys combined with mutagenic studies support a toggle model for photoconversion that engages multiple features within the PSM to stabilize the Pr and Pfr end states after rotation of the D pyrrole ring. Taken together, this Arabidopsis PhyB structure should enable molecular insights into plant Phy signaling and provide an essential scaffold to redesign their activities for agricultural benefit and as optogenetic reagents.

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Organizational Affiliation: 
• Department of Genetics, University of Wisconsin-Madison, Madison, WI 53706.
Department of Genetics, University of Wisconsin-Madison, Madison, WI 53706 [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 122.83 kDa 
• Atom Count: 7,100 
• Modeled Residue Count: 893 
• Deposited Residue Count: 1,088 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytochrome B	A	544	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At2g18790, HY3, MSF3.17, PHYB
UniProt
Find proteins for P14713 (Arabidopsis thaliana) Explore P14713  Go to UniProtKB:  P14713

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytochrome B	B	544	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PHYB, HY3, At2g18790, MSF3.17
UniProt
Find proteins for P14713 (Arabidopsis thaliana) Explore P14713  Go to UniProtKB:  P14713

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O6E	K [auth A], R [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
PGE	Q [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], P [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth A], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free:  0.270 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.502	α = 90
b = 127.502	β = 90
c = 300.772	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Sethe Burgie, E., Bussell, A.N., Walker, J.M., Dubiel, K., Vierstra, R.D.

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2014-07-30
  Changes: Database references
• Version 2.0: 2021-10-13
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary