6RYI

WUS-HD bound to G-Box DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1038/s41467-020-16024-y
  • Primary Citation of Related Structures:  
    6RY3, 6RYD, 6RYI, 6RYL

  • 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 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

    Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein WUSCHEL
A, B, C, D, E
76Arabidopsis thalianaMutation(s): 0 
Gene Names: WUSPGA6At2g17950T27K22.18
UniProt
Find proteins for Q9SB92 (Arabidopsis thaliana)
Explore Q9SB92 
Go to UniProtKB:  Q9SB92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SB92
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*CP*GP*TP*CP*AP*CP*GP*TP*GP*AP*TP*GP*GP*G)-3')
F, H
16Arabidopsis thaliana
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*CP*CP*AP*TP*CP*AP*CP*GP*TP*GP*AP*CP*GP*AP*C)-3')
G, I
16Arabidopsis thaliana
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.434α = 90
b = 83.068β = 112.95
c = 85.651γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-05-20
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description