4NBM

Crystal structure of UVB photoreceptor UVR8 and light-induced structural changes at 180K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Dynamic Crystallography Reveals Early Signalling Events in Ultraviolet Photoreceptor UVR8.

Zeng, X.Ren, Z.Wu, Q.Fan, J.Peng, P.P.Tang, K.Zhang, R.Zhao, K.H.Yang, X.

(2015) Nat Plants 1

  • DOI: https://doi.org/10.1038/nplants.2014.6
  • Primary Citation of Related Structures:  
    4NAA, 4NBM, 4NC4

  • PubMed Abstract: 

    Arabidopsis thaliana UVR8 ( At UVR8) is a long-sought-after photoreceptor that undergoes dimer dissociation in response to UV-B light. Crystallographic and mutational studies have identified two crucial tryptophan residues for UV-B responses in At UVR8. However, the mechanism of UV-B perception and structural events leading up to dimer dissociation remain elusive at the molecular level. We applied dynamic crystallography to capture light-induced structural events in photoactive At UVR8 crystals. Here we report two intermediate structures at 1.67Å resolution. At the epicenter of UV-B signaling, concerted motions associated with Trp285/Trp233 lead to ejection of a water molecule, which weakens an intricate network of hydrogen bonds and salt bridges at the dimer interface. Partial opening of the β-propeller structure due to thermal relaxation of conformational strains originating in the epicenter further disrupts the dimer interface and leads to dimer dissociation. These dynamic crystallographic observations provide structural insights into the photo-perception and signaling mechanism of UVR8.


  • Organizational Affiliation

    Key State Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, P.R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ultraviolet-B receptor UVR8
A, B, C, D
377Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g63860MGI19.7UVR8
UniProt
Find proteins for Q9FN03 (Arabidopsis thaliana)
Explore Q9FN03 
Go to UniProtKB:  Q9FN03
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FN03
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
AA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.31α = 90
b = 76.828β = 96.75
c = 191.253γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations