6RYD

WUS-HD bound to TGAA DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL.

Sloan, J.Hakenjos, J.P.Gebert, M.Ermakova, O.Gumiero, A.Stier, G.Wild, K.Sinning, I.Lohmann, J.U.

(2020) Nat Commun 11: 2223-2223

  • DOI: 10.1038/s41467-020-16024-y
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Stem cells are one of the foundational evolutionary novelties that allowed the independent emergence of multicellularity in the plant and animal lineages. In plants, the homeodomain (HD) transcription factor WUSCHEL (WUS) is essential for the mainten ...

    Stem cells are one of the foundational evolutionary novelties that allowed the independent emergence of multicellularity in the plant and animal lineages. In plants, the homeodomain (HD) transcription factor WUSCHEL (WUS) is essential for the maintenance of stem cells in the shoot apical meristem. WUS has been reported to bind to diverse DNA motifs and to act as transcriptional activator and repressor. However, the mechanisms underlying this remarkable behavior have remained unclear. Here, we quantitatively delineate WUS binding to three divergent DNA motifs and resolve the relevant structural underpinnings. We show that WUS exhibits a strong binding preference for TGAA repeat sequences, while retaining the ability to weakly bind to TAAT elements. This behavior is attributable to the formation of dimers through interactions of specific residues in the HD that stabilize WUS DNA interaction. Our results provide a mechanistic basis for dissecting WUS dependent regulatory networks in plant stem cell control.


    Organizational Affiliation

    Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany. jan.lohmann@cos.uni-heidelberg.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein WUSCHEL
A, B, E, F
76Arabidopsis thalianaMutation(s): 0 
Gene Names: WUSPGA6At2g17950T27K22.18
Find proteins for Q9SB92 (Arabidopsis thaliana)
Go to UniProtKB:  Q9SB92
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*TP*GP*TP*AP*TP*GP*AP*AP*TP*GP*AP*AP*CP*G)-3')C, G16Arabidopsis thaliana
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*TP*CP*AP*TP*TP*CP*AP*TP*AP*CP*AP*CP*T)-3')D, H16Arabidopsis thaliana
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.74α = 90
b = 54.34β = 107.54
c = 75.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History 

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references