Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 114.33 kDa 
• Atom Count: 7502 
• Modelled Residue Count: 969 
• Deposited Residue Count: 1046 
• Unique protein chains: 1

4O0P

Crystal Structure of D. radiodurans Bacteriophytochrome Photosensory Core Module in its Dark Form

• DOI: 10.2210/pdb4O0P/pdb

• Classification: TRANSFERASE
• Organism(s): Deinococcus radiodurans R1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-14 Released: 2014-05-07 
• Deposition Author(s): Takala, H., Ihalainen, J.A., Westenhoff, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.266 
• R-Value Work: 0.253 
• R-Value Observed: 0.254 

Literature

Signal amplification and transduction in phytochrome photosensors

Takala, H., Bjorling, A., Berntsson, O., Lehtivuori, H., Niebling, S., Hoernke, M., Kosheleva, I., Henning, R., Menzel, A., Ihalainen, J.A., Westenhoff, S.

(2014) Nature 509: 245-248

• PubMed: 24776794 
• DOI: 10.1038/nature13310
• Primary Citation of Related Structures:  
  4O01, 4O0P


• PubMed Abstract: 
  

Sensory proteins must relay structural signals from the sensory site over large distances to regulatory output domains. Phytochromes are a major family of red-light-sensing kinases that control diverse cellular functions in plants, bacteria and fungi. Bacterial phytochromes consist of a photosensory core and a carboxy-terminal regulatory domain. Structures of photosensory cores are reported in the resting state and conformational responses to light activation have been proposed in the vicinity of the chromophore. However, the structure of the signalling state and the mechanism of downstream signal relay through the photosensory core remain elusive. Here we report crystal and solution structures of the resting and activated states of the photosensory core of the bacteriophytochrome from Deinococcus radiodurans. The structures show an open and closed form of the dimeric protein for the activated and resting states, respectively. This nanometre-scale rearrangement is controlled by refolding of an evolutionarily conserved 'tongue', which is in contact with the chromophore. The findings reveal an unusual mechanism in which atomic-scale conformational changes around the chromophore are first amplified into an ångstrom-scale distance change in the tongue, and further grow into a nanometre-scale conformational signal. The structural mechanism is a blueprint for understanding how phytochromes connect to the cellular signalling network.

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Organizational Affiliation: 

Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriophytochrome	A, B	523	Deinococcus radiodurans R1	Mutation(s): 0  Gene Names: bphP, DR_A0050 EC: 2.7.13.3
UniProt
Find proteins for Q9RZA4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Explore Q9RZA4  Go to UniProtKB:  Q9RZA4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LBV (Subject of Investigation/LOI)	C [auth A], D [auth B]	3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid C33 H37 N4 O6 DKMLMZVDTGOEGU-ISEYCTJISA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.266 
• R-Value Work: 0.253 
• R-Value Observed: 0.254 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.28	α = 90
b = 150.28	β = 90
c = 145.95	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2013-12-14 
• Released Date: 2014-05-07 
Deposition Author(s): Takala, H., Ihalainen, J.A., Westenhoff, S.

Revision History  

• Version 1.0: 2014-05-07
  Type: Initial release
  
• Version 1.1: 2014-05-14
  Changes: Database references