6XZM | pdb_00006xzm

Arabidopsis UV-B photoreceptor UVR8 mutant D96N D107N W285A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.248 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.197 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6XZM

This is version 1.3 of the entry. See complete history

Literature

A constitutively monomeric UVR8 photoreceptor confers enhanced UV-B photomorphogenesis.

Podolec, R.Lau, K.Wagnon, T.B.Hothorn, M.Ulm, R.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2017284118
  • Primary Citation Related Structures: 
    6XZL, 6XZM, 6XZN

  • PubMed Abstract: 

    The plant ultraviolet-B (UV-B) photoreceptor UVR8 plays an important role in UV-B acclimation and survival. UV-B absorption by homodimeric UVR8 induces its monomerization and interaction with the E3 ubiquitin ligase COP1, leading ultimately to gene expression changes. UVR8 is inactivated through redimerization, facilitated by RUP1 and RUP2. Here, we describe a semidominant, hyperactive allele, namely uvr8-17D , that harbors a glycine-101 to serine mutation. UVR8 G101S overexpression led to weak constitutive photomorphogenesis and extreme UV-B responsiveness. UVR8 G101S was observed to be predominantly monomeric in vivo and, once activated by UV-B, was not efficiently inactivated. Analysis of a UVR8 crystal structure containing the G101S mutation revealed the distortion of a loop region normally involved in stabilization of the UVR8 homodimer. Plants expressing a UVR8 variant combining G101S with the previously described W285A mutation exhibited robust constitutive photomorphogenesis. This work provides further insight into UVR8 activation and inactivation mechanisms and describes a genetic tool for the manipulation of photomorphogenic responses.


  • Organizational Affiliation
    • Department of Botany and Plant Biology, Section of Biology, Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 80.9 kDa 
  • Atom Count: 5,621 
  • Modeled Residue Count: 734 
  • Deposited Residue Count: 746 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ultraviolet-B receptor UVR8
A, B
373Arabidopsis thalianaMutation(s): 3 
Gene Names: UVR8At5g63860MGI19.7
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
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE

Query on PGE



Download:Ideal Coordinates CCD File
J [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
I [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
NO3

Query on NO3



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
F [auth B],
G [auth B]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.248 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.197 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.266α = 90
b = 98.266β = 90
c = 138.836γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_175774
European Research Council (ERC)Switzerland310539

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary