4D9S | pdb_00004d9s

Crystal structure of Arabidopsis thaliana UVR8 (UV Resistance locus 8)

• PDB DOI: https://doi.org/10.2210/pdb4D9S/pdb

• Classification: chromatin-binding protein
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-11 Released: 2012-04-04 
• Deposition Author(s): Arvai, A.S., Christie, J.M., Pratt, A.J., Hitomi, K., Getzoff, E.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.194 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Plant UVR8 Photoreceptor Senses UV-B by Tryptophan-Mediated Disruption of Cross-Dimer Salt Bridges.

Christie, J.M., Arvai, A.S., Baxter, K.J., Heilmann, M., Pratt, A.J., O'Hara, A., Kelly, S.M., Hothorn, M., Smith, B.O., Hitomi, K., Jenkins, G.I., Getzoff, E.D.

(2012) Science 335: 1492-1496

• PubMed: 22323738 
• DOI: https://doi.org/10.1126/science.1218091
• Primary Citation Related Structures: 
  4D9S


• PubMed Abstract: 
  

  The recently identified plant photoreceptor UVR8 (UV RESISTANCE LOCUS 8) triggers regulatory changes in gene expression in response to ultraviolet-B (UV-B) light through an unknown mechanism. Here, crystallographic and solution structures of the UVR8 homodimer, together with mutagenesis and far-UV circular dichroism spectroscopy, reveal its mechanisms for UV-B perception and signal transduction. β-propeller subunits form a remarkable, tryptophan-dominated, dimer interface stitched together by a complex salt-bridge network. Salt-bridging arginines flank the excitonically coupled cross-dimer tryptophan "pyramid" responsible for UV-B sensing. Photoreception reversibly disrupts salt bridges, triggering dimer dissociation and signal initiation. Mutation of a single tryptophan to phenylalanine retunes the photoreceptor to detect UV-C wavelengths. Our analyses establish how UVR8 functions as a photoreceptor without a prosthetic chromophore to promote plant development and survival in sunlight.

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Organizational Affiliation: 
• Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87.1 kDa 
• Atom Count: 6,661 
• Modeled Residue Count: 763 
• Deposited Residue Count: 812 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UVB-resistance protein UVR8	A, B	406	Arabidopsis thaliana	Mutation(s): 0  Gene Names: UVR8, At5g63860
UniProt
Find proteins for Q9FN03 (Arabidopsis thaliana) Explore Q9FN03  Go to UniProtKB:  Q9FN03

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.194 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.117	α = 90
b = 51.511	β = 102.89
c = 97.084	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Arvai, A.S., Christie, J.M., Pratt, A.J., Hitomi, K., Getzoff, E.D.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description